From 8d191d43cd612e6ce04defc9fdd0205a87a3f6b0 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 24 Jan 2024 11:29:48 -0800 Subject: [PATCH 01/23] Started implementing pharokka --- conf/test.config | 6 +- conf/test_data.config | 820 ++++++++++++++++-- modules.json | 10 + modules/local/prodigal/prodigalgv/main.nf | 2 + .../prodigal/prodigalgv/tests/main.nf.test | 1 + .../prodigalgv/tests/main.nf.test.snap | 2 +- modules/nf-core/mash/screen/nextflow.config | 1 - .../pharokka/installdatabases/environment.yml | 9 + .../nf-core/pharokka/installdatabases/main.nf | 81 ++ .../pharokka/installdatabases/meta.yml | 34 + .../pharokka/installdatabases/nextflow.config | 3 + .../installdatabases/tests/main.nf.test | 22 + .../installdatabases/tests/main.nf.test.snap | 103 +++ .../pharokka/installdatabases/tests/tags.yml | 2 + .../nf-core/pharokka/pharokka/environment.yml | 9 + modules/nf-core/pharokka/pharokka/main.nf | 68 ++ modules/nf-core/pharokka/pharokka/meta.yml | 71 ++ .../nf-core/pharokka/pharokka/nextflow.config | 12 + .../pharokka/pharokka/tests/main.nf.test | 46 + .../pharokka/pharokka/tests/main.nf.test.snap | 26 + .../pharokka/pharokka/tests/nextflow.config | 8 + .../nf-core/pharokka/pharokka/tests/tags.yml | 2 + nextflow.config | 13 +- .../fasta_microdiversity_instrain/main.nf | 21 +- .../fasta_phage_function_pharokka/main.nf | 38 + .../nextflow.config | 2 + .../tests/main.nf.test | 32 + .../tests/main.nf.test.snap | 27 + .../tests/nextflow.config | 5 + .../tests/pharokka_db_provided.test | 34 + .../tests/tags.yml | 2 + .../local/fasta_phage_host_iphop/main.nf | 16 +- .../local/fasta_virus_quality_checkv/main.nf | 7 - test.faa | 101 +++ workflows/phageannotator/main.nf | 49 +- workflows/phageannotator/nextflow.config | 1 + .../phageannotator/tests/main.nf.test.snap | 84 +- .../tests/skip_bacphlip.nf.test.snap | 84 +- .../tests/skip_checkv.nf.test.snap | 84 +- .../tests/skip_genomad.nf.test.snap | 84 +- .../tests/skip_genomad_taxonomy.nf.test.snap | 84 +- .../tests/skip_instrain.nf.test.snap | 50 +- .../tests/skip_iphop.nf.test.snap | 82 +- ...odigalgv.nf.test => skip_pharokka.nf.test} | 6 +- ...f.test.snap => skip_pharokka.nf.test.snap} | 0 .../skip_reference_containment.nf.test.snap | 84 +- .../tests/skip_viromeqc.nf.test.snap | 84 +- .../tests/skip_virus_clustering.nf.test.snap | 72 +- workflows/phageannotator/tests/tags.yml | 2 +- 49 files changed, 1746 insertions(+), 740 deletions(-) create mode 100644 modules/nf-core/pharokka/installdatabases/environment.yml create mode 100644 modules/nf-core/pharokka/installdatabases/main.nf create mode 100644 modules/nf-core/pharokka/installdatabases/meta.yml create mode 100644 modules/nf-core/pharokka/installdatabases/nextflow.config create mode 100644 modules/nf-core/pharokka/installdatabases/tests/main.nf.test create mode 100644 modules/nf-core/pharokka/installdatabases/tests/main.nf.test.snap create mode 100644 modules/nf-core/pharokka/installdatabases/tests/tags.yml create mode 100644 modules/nf-core/pharokka/pharokka/environment.yml create mode 100644 modules/nf-core/pharokka/pharokka/main.nf create mode 100644 modules/nf-core/pharokka/pharokka/meta.yml create mode 100644 modules/nf-core/pharokka/pharokka/nextflow.config create mode 100644 modules/nf-core/pharokka/pharokka/tests/main.nf.test create mode 100644 modules/nf-core/pharokka/pharokka/tests/main.nf.test.snap create mode 100644 modules/nf-core/pharokka/pharokka/tests/nextflow.config create mode 100644 modules/nf-core/pharokka/pharokka/tests/tags.yml create mode 100644 subworkflows/local/fasta_phage_function_pharokka/main.nf create mode 100644 subworkflows/local/fasta_phage_function_pharokka/nextflow.config create mode 100644 subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test create mode 100644 subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap create mode 100644 subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config create mode 100644 subworkflows/local/fasta_phage_function_pharokka/tests/pharokka_db_provided.test create mode 100644 subworkflows/local/fasta_phage_function_pharokka/tests/tags.yml create mode 100644 test.faa rename workflows/phageannotator/tests/{skip_prodigalgv.nf.test => skip_pharokka.nf.test} (93%) rename workflows/phageannotator/tests/{skip_prodigalgv.nf.test.snap => skip_pharokka.nf.test.snap} (100%) diff --git a/conf/test.config b/conf/test.config index c8b4628..afd97ff 100644 --- a/conf/test.config +++ b/conf/test.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function ' // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' + //max_cpus = 2 + //max_memory = '6.GB' max_time = '6.h' // Input data @@ -30,5 +30,3 @@ params { // Pipeline options publish_dir_mode = 'symlink' } - -includeConfig './test_data.config' diff --git a/conf/test_data.config b/conf/test_data.config index a4f0a88..1312d89 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -1,11 +1,14 @@ +// README: +// https://github.com/nf-core/test-datasets/blob/modules/README.md + params { // Base directory for test data - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" + nf_core_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" + phageannotator_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" - // TODO: Add all test data to test_data.config test_data { 'assets' { - test_samplesheet = "${params.test_data_base}/assets/1.0.0/test_samplesheet.csv" + test_samplesheet = "${params.phageannotator_test_data_base}/assets/1.0.0/test_samplesheet.csv" } 'generic' { 'tar' { @@ -13,74 +16,793 @@ params { } } 'modules_local' { - assembly_fasta_gz = "${params.test_data_base}/modules/local/seqkit/seq/assembly.fasta.gz" - mash_sketch1_msh = "${params.test_data_base}/modules/local/mash/paste/bacteroides_fragilis_contigs1.msh" - mash_sketch2_msh = "${params.test_data_base}/modules/local/mash/paste/bacteroides_fragilis_contigs2.msh" - reference_fasta_gz = "${params.test_data_base}/modules/local/append_screen_hits/reference.fasta.gz" - mash_screen_results_tsv = "${params.test_data_base}/modules/local/append_screen_hits/mash_screen_results.tsv" - virus_summary1_tsv = "${params.test_data_base}/modules/local/awk/test1_virus_summary.tsv" - virus_summary2_tsv = "${params.test_data_base}/modules/local/awk/test2_virus_summary.tsv" - viruses_fna_gz = "${params.test_data_base}/modules/local/quality_filter_viruses/viruses.fna.gz" - proviruses_fna_gz = "${params.test_data_base}/modules/local/quality_filter_viruses/proviruses.fna.gz" - quality_summary_tsv = "${params.test_data_base}/modules/local/quality_filter_viruses/quality_summary.tsv" - blast_txt = "${params.test_data_base}/modules/local/anicluster/anicalc/blast.txt" - ani_tsv = "${params.test_data_base}/modules/local/anicluster/aniclust/ani.tsv" - clusters_tsv = "${params.test_data_base}/modules/local/anicluster/extractreps/clusters.tsv" + assembly_fasta_gz = "${params.phageannotator_test_data_base}/modules/local/seqkit/seq/assembly.fasta.gz" + mash_sketch1_msh = "${params.phageannotator_test_data_base}/modules/local/mash/paste/bacteroides_fragilis_contigs1.msh" + mash_sketch2_msh = "${params.phageannotator_test_data_base}/modules/local/mash/paste/bacteroides_fragilis_contigs2.msh" + reference_fasta_gz = "${params.phageannotator_test_data_base}/modules/local/append_screen_hits/reference.fasta.gz" + mash_screen_results_tsv = "${params.phageannotator_test_data_base}/modules/local/append_screen_hits/mash_screen_results.tsv" + virus_summary1_tsv = "${params.phageannotator_test_data_base}/modules/local/awk/test1_virus_summary.tsv" + virus_summary2_tsv = "${params.phageannotator_test_data_base}/modules/local/awk/test2_virus_summary.tsv" + viruses_fna_gz = "${params.phageannotator_test_data_base}/modules/local/quality_filter_viruses/viruses.fna.gz" + proviruses_fna_gz = "${params.phageannotator_test_data_base}/modules/local/quality_filter_viruses/proviruses.fna.gz" + quality_summary_tsv = "${params.phageannotator_test_data_base}/modules/local/quality_filter_viruses/quality_summary.tsv" + blast_txt = "${params.phageannotator_test_data_base}/modules/local/anicluster/anicalc/blast.txt" + ani_tsv = "${params.phageannotator_test_data_base}/modules/local/anicluster/aniclust/ani.tsv" + clusters_tsv = "${params.phageannotator_test_data_base}/modules/local/anicluster/extractreps/clusters.tsv" } 'modules_nfcore' { - checkv_test_db_tar = "${params.test_data_base}/modules/nfcore/checkv/endtoend/checkv_minimal_db.tar" - iphop_test_db_tar_gz = "${params.test_data_base}/modules/nfcore/iphop/download/Test_db_rw.tar.gz" - iphop_data_tar_gz = "${params.test_data_base}/modules/nfcore/iphop/predict/iPHoP_data.tar.gz" - instrain_stb = "${params.test_data_base}/modules/nfcore/instrain/profile/instrain_stb.stb" - proteins_fna_gz = "${params.test_data_base}/modules/nfcore/instrain/profile/proteins.fna.gz" + checkv_test_db_tar = "${params.phageannotator_test_data_base}/modules/nfcore/checkv/endtoend/checkv_minimal_db.tar" + iphop_test_db_tar_gz = "${params.phageannotator_test_data_base}/modules/nfcore/iphop/download/Test_db_rw.tar.gz" + iphop_data_tar_gz = "${params.phageannotator_test_data_base}/modules/nfcore/iphop/predict/iPHoP_data.tar.gz" + instrain_stb = "${params.phageannotator_test_data_base}/modules/nfcore/instrain/profile/instrain_stb.stb" + proteins_fna_gz = "${params.phageannotator_test_data_base}/modules/nfcore/instrain/profile/proteins.fna.gz" } 'workflows' { 'phageannotator' { - sars_cov2_contigs_fasta_gz = "${params.test_data_base}/workflows/phageannotator/sars_cov2_contigs.fasta.gz" + sars_cov2_contigs_fasta_gz = "${params.phageannotator_test_data_base}/workflows/phageannotator/sars_cov2_contigs.fasta.gz" } } 'sarscov2' { + 'genome' { + genome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta" + genome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz" + genome_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai" + genome_fasta_txt_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst" + genome_dict = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.dict" + genome_gff3 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gff3" + genome_gff3_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz" + genome_gtf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gtf" + genome_paf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.paf" + genome_sizes = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.sizes" + transcriptome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta" + transcriptome_paf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf" + proteome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/proteome.fasta" + proteome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz" + + test_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed" + test_bed_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz" + test2_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed" + test_bed12 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12" + baits_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed" + bed_autosql = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as" + + reference_cnn = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn" + + kraken2 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2" + kraken2_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + + kraken2_bracken = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken" + kraken2_bracken_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" + + kaiju = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kaiju" + kaiju_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz" + + kofamscan_profiles_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" + kofamscan_ko_list_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" + + ncbi_taxmap_zip = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" + taxon_list_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" + + mmseqs_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz" + + resfinder_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz" + + all_sites_fas = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas" + informative_sites_fas = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas" + + contigs_genome_maf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" + contigs_genome_par = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par" + lastdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" + + baits_interval_list = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list" + targets_interval_list = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list" + regions_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt" + lc_extrap_mr = "${params.nf_core_test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr" + } 'illumina' { - test_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" - test2_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" - contigs_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/contigs.fasta" - scaffolds_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" - test_single_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.single_end.bam" - test_paired_end_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" - test_1_fastq_gz_fastqc_zip = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + test_single_end_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_single_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" + test_single_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" + test_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_methylated_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" + test_paired_end_methylated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" + test_paired_end_methylated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" + test_unaligned_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam" + + test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" + test_interleaved_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" + test_1_fastq_txt_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst" + test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" + test_methylated_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" + test_methylated_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" + test_1_fastq_gz_fastqc_html = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html" + test_1_fastq_gz_fastqc_zip = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + + test_bedgraph = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph" + + test_bigwig = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig" + + test_wig_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz" + + test_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" + + test_computematrix_mat_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" + + test_bcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf" + + test_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf" + test_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz" + test_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" + test2_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf" + test2_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + test2_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + test2_vcf_targets_tsv_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" + test3_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf" + test3_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz" + test3_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" + + contigs_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta" + scaffolds_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" + + assembly_gfa = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa" + assembly_gfa_bgz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" + assembly_gfa_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" + assembly_gfa_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" + + test_single_end_bam_readlist_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" + + SRR13255544_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + SRR11140744_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" } + 'nanopore' { + test_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam" + test_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" + + fast5_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" + + test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz" + + test_sequencing_summary = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" + } + 'metagenome' { + classified_reads_assignment = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" + kraken_report = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" + krona_taxonomy = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab" + seqid2taxid_map = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map" + nodes_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp" + names_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/names.dmp" + prot_nodes_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp" + prot_names_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp" + prot_accession2taxid_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz" + } + } + 'mus_musculus' { 'genome' { - genome_fasta_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.gz" - genome_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta" - kraken2_tar_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + rnaseq_samplesheet = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" + rnaseq_genemeta = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" + rnaseq_contrasts = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" + rnaseq_matrix = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" + rnaseq_lengths = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv" + deseq_results = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" + genome_19_fasta = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz" + genome_19_gtf = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz" + } + 'illumina' { + test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" + test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" + genome_config = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json" + multiome_lib_csv = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv" + test_scARC_gex_R1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_gex_R2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_R1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_atac_R2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_I2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz" + } + 'csv' { + count_table = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv" + library = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv" + } + 'txt' { + design_matrix = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt" } } 'homo_sapiens' { - 'illumina' { - test_flowcell = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" - test_paired_end_sorted_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" - test2_paired_end_sorted_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + '10xgenomics' { + cellranger { + test_10x_10k_pbmc_5fb_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5fb_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv" + + test_10x_10k_pbmc_cmo_cmo_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_cmo_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv" + + test_10x_5k_cmvpos_tcells_ab_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_ab_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" + + test_10x_vdj_ref_json = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json" + test_10x_vdj_ref_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa" + test_10x_vdj_ref_suppfasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa" + + test_scATAC_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz" + test_scATAC_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz" + test_scATAC_3_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz" + test_scATAC_I_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz" + } + spaceranger { + test_10x_ffpe_cytassist_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_cytassist_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_cytassist_image = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif" + test_10x_ffpe_cytassist_probeset = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv" + + test_10x_ffpe_v1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_v1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_v1_image = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" + } } 'genome' { - genome_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" - genome_fasta_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta.gz" - transcriptome_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/transcriptome.fasta" + genome_elfasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta" + genome_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta" + genome_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" + genome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz" + genome_fasta_gz_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai" + genome_fasta_gz_gzi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi" + genome_strtablefile = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip" + genome_dict = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.dict" + genome_gff3 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3" + genome_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf" + genome_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list" + genome_multi_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed" + genome_blacklist_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed" + genome_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes" + genome_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed" + genome_header = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.header" + genome_bed_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz" + genome_bed_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi" + genome_elsites = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites" + transcriptome_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta" + genome2_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta" + genome_chain_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz" + genome_annotated_interval_tsv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv" + genome_mt_gb = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb" + genome_preprocessed_count_tsv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv" + genome_preprocessed_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list" + genome_ploidy_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz" + genome_ploidy_calls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz" + genome_germline_cnv_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz" + genome_germline_cnv_calls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz" + genome_motifs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt" + genome_config = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json" + + genome_1_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz" + genome_1_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf" + + genome_21_sdf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" + genome_21_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + genome_21_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + genome_21_gencode_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf" + genome_21_dict = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" + genome_21_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_annotated_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed" + genome_21_multi_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_antitarget_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" + genome_21_multi_interval_bed_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" + genome_21_chromosomes_dir = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + genome_21_reference_cnn = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" + genome_21_eigenstrat_snp = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp" + genome_21_stitch_posfile = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv" + + dbsnp_146_hg38_elsites = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" + dbsnp_146_hg38_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_146_hg38_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + gnomad_r2_1_1_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + mills_and_1000g_indels_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + syntheticvcf_short_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" + syntheticvcf_short_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + syntheticvcf_short_score = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" + gnomad_r2_1_1_sv_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" + gnomad2_r2_1_1_sv_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" + + hapmap_3_3_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" + res_1000g_omni2_5_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" + res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" + res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" + res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" + dbsnp_138_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_138_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + gnomad_r2_1_1_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + mills_and_1000g_indels_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + haplotype_map = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" + dbNSFP_4_1a_21_hg38_txt_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz" + dbNSFP_4_1a_21_hg38_txt_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi" + ngscheckmate_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" + + index_salmon = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/index/salmon" + repeat_expansions = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json" + justhusky_ped = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" + justhusky_minimal_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" + justhusky_minimal_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" + + vcfanno_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" + vcfanno_toml = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" + updsites_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed" + + prg_input = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip" + crispr_functional_counts = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv" + crispr_functional_library = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv" + + vep_cache = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz" + affy_array_samplesheet = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv" + affy_array_celfiles_tar = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar" + + } + 'pangenome' { + pangenome_fa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa" + pangenome_fa_bgzip = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz" + pangenome_fa_bgzip_fai = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai" + pangenome_fa_bgzip_gzi = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" + pangenome_paf = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf" + pangenome_paf_gz = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz" + pangenome_panacus_tsv = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv" + pangenome_seqwish_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa" + pangenome_smoothxg_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" + pangenome_gfaffix_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" + 'odgi' { + pangenome_og = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og" + pangenome_lay = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay" + } + } + 'illumina' { + test_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_name_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" + test_paired_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" + test_paired_end_markduplicates_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" + test_paired_end_markduplicates_sorted_referencesn_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" + test_paired_end_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" + test_paired_end_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" + test_paired_end_umi_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" + test_paired_end_umi_converted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" + test_paired_end_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" + test_paired_end_umi_histogram_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" + test_paired_end_umi_unsorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" + test_paired_end_umi_unsorted_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + test_paired_end_hla = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" + test_paired_end_hla_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" + test_paired_end_hla_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" + test_rna_paired_end_sorted_chr6_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam" + test_rna_paired_end_sorted_chr6_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai" + + test2_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" + test2_paired_end_name_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" + test2_paired_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" + test2_paired_end_markduplicates_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" + test2_paired_end_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" + test2_paired_end_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" + test2_paired_end_umi_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" + test2_paired_end_umi_converted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" + test2_paired_end_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" + test2_paired_end_umi_histogram_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" + test2_paired_end_umi_unsorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" + test2_paired_end_umi_unsorted_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + test_paired_end_duplex_umi_unmapped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" + test_paired_end_duplex_umi_mapped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" + test_paired_end_duplex_umi_mapped_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" + test_paired_end_duplex_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" + test_paired_end_duplex_umi_duplex_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" + + mitochon_standin_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" + mitochon_standin_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" + test_illumina_mt_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam" + test_illumina_mt_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai" + + test3_single_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" + + read_group_settings_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" + + test_paired_end_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" + test_paired_end_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" + test_paired_end_markduplicates_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" + test_paired_end_markduplicates_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" + test_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" + test_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" + + test2_paired_end_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" + test2_paired_end_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" + test2_paired_end_markduplicates_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" + test2_paired_end_markduplicates_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" + test2_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" + test2_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" + test3_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram" + test3_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai" + + test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" + test_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" + test_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" + test_airrseq_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz" + test_airrseq_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz" + test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" + test2_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" + test2_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" + test_rnaseq_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" + test_rnaseq_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" + test_paired_end_duplex_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" + test_paired_end_duplex_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" + + test_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" + test2_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + test_pileups_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table" + test2_pileups_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" + + test_paired_end_sorted_dragstrmodel = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" + + test_genomicsdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" + test_pon_genomicsdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" + + test2_haplotc_ann_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" + test2_haplotc_ann_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test_haplotc_cnn_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" + test_haplotc_cnn_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" + + test2_haplotc_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" + test2_haplotc_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" + + test2_recal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" + test2_recal_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" + test2_tranches = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" + test2_allele_specific_recal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" + test2_allele_specific_recal_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" + test2_allele_specific_tranches = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" + + test_test2_paired_mutect2_calls_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" + test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" + test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" + test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" + test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" + test_test2_paired_segmentation_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" + test_test2_paired_contamination_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" + + test_genome_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" + test_genome_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" + test_genome_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" + test_genome_vcf_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" + + test_genome_vcf_ud = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" + test_genome_vcf_mu = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" + test_genome_vcf_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" + + test2_genome_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" + test2_genome_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" + test2_genome_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" + test2_genome_vcf_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + + test_genome21_indels_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + + test_mpileup = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" + test2_mpileup = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" + + test_broadpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" + test2_broadpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" + + test_narrowpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" + test2_narrowpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" + + test_yak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak" + test2_yak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak" + + cutandrun_bedgraph_test_1 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" + cutandrun_bedgraph_test_2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" + na24385_chr22_coverage = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed" + + empty_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz" + empty_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi" + + simulated_sv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz" + simulated_sv_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi" + simulated_sv2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz" + simulated_sv2_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi" + + test_rnaseq_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" + test_sv_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" + test_sv_vcf_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi" + na24385_chr22_sv_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz" + na24385_chr22_sv_vcf_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi" + genmod_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" + genmod_annotate_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" + genmod_models_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" + genmod_score_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" + + test_mito_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" + + test_pytor = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor" + rank_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" + + test_flowcell = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" + test_flowcell_samplesheet = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" + + varlociraptor_scenario = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml" + + contig_ploidy_priors_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" + + purecn_ex1_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam" + purecn_ex1_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai" + purecn_ex1_interval = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt" + purecn_ex1_normal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz" + purecn_ex2_normal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz" + purecn_normalpanel_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz" + purecn_normalpanel_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi" + } + 'pacbio' { + primers = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta" + alz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam" + alzpbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" + ccs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" + ccs_fa = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" + ccs_fa_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" + ccs_fq = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" + ccs_fq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" + ccs_xml = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" + hifi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" + lima = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" + refine = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" + cluster = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" + singletons = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" + aligned = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" + alignedbai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" + genemodel1 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" + genemodel2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" + filelist = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt" + } + 'scramble' { + fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.fa" + fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai" + bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bam" + bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai" + cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.cram" + cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai" + bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bed" + } + 'gene_set_analysis' { + gct = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct" + cls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls" + gmx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx" + } + 'cnvkit' { + amplicon_cnr = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr" + amplicon_cns = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns" } } 'bacteroides_fragilis' { + 'genome' { + genome_fna_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_gbff_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" + genome_paf = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" + genome_gff_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" + + } + 'hamronization' { + genome_abricate_tsv = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" + genome_mapping_potential_arg = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" + } + 'illumina' { + test1_contigs_fa_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" + test1_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" + test1_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" + test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" + test1_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" + test1_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" + test1_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" + test2_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" + test2_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" + } + 'nanopore' { + test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" + overlap_paf = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" + } + } + 'candidatus_portiera_aleyrodidarum' { + 'genome' { + //genome_fasta = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" + genome_sizes = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" + genome_aln_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" + genome_aln_nwk = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" + proteome_fasta = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" + test1_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" + test2_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" + test3_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" + } 'illumina' { - test1_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" - test1_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" - test2_1_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" - contigs_fa_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" - test1_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" - test2_bam = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" + test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" + test_se_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" } + 'nanopore' { + test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" + } + } + 'haemophilus_influenzae' { 'genome' { - genome_fna_gz = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_fna_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" + genome_aln_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" + genome_aln_nwk = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" + } + } + 'generic' { + 'csv' { + test_csv = "${params.nf_core_test_data_base}/data/generic/csv/test.csv" + } + 'notebooks' { + rmarkdown = "${params.nf_core_test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" + ipython_md = "${params.nf_core_test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md" + ipython_ipynb = "${params.nf_core_test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb" + } + 'tar' { + tar_gz = "${params.nf_core_test_data_base}/data/generic/tar/hello.tar.gz" + } + 'tsv' { + test_tsv = "${params.nf_core_test_data_base}/data/generic/tsv/test.tsv" + } + 'txt' { + hello = "${params.nf_core_test_data_base}/data/generic/txt/hello.txt" + } + 'cooler'{ + test_pairix_pair_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" + test_pairix_pair_gz_px2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" + test_pairs_pair = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" + test_tabix_pair_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" + test_tabix_pair_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" + hg19_chrom_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" + test_merge_cool = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" + test_merge_cool_cp2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" + + } + 'pairtools' { + mock_4dedup_pairsam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam" + mock_4flip_pairs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs" + mock_chrom_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes" + mock_pairsam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam" + mock_sam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam" + frag_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed" + } + 'estsfs'{ + config_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/config-JC.txt" + data_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT" + seed_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/seedfile.txt" + } + 'config' { + ncbi_user_settings = "${params.nf_core_test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + } + 'unsorted_data' { + 'unsorted_text' { + genome_file = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome" + intervals = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed" + numbers_csv = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv" + } + } + } + 'proteomics' { + 'msspectra' { + ups_file1 = "${params.nf_core_test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw" + ups_file2 = "${params.nf_core_test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw" + profile_spectra = "${params.nf_core_test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML" + hla2_file = "${params.nf_core_test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw" + } + 'database' { + yeast_ups = "${params.nf_core_test_data_base}/data/proteomics/database/yeast_UPS.fasta" + } + 'maxquant' { + mq_contrasts = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" + mq_proteingroups = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt" + mq_samplesheet = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv" + mq_proteus_mat = "${params.nf_core_test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv" + } + 'parameter' { + maxquant = "${params.nf_core_test_data_base}/data/proteomics/parameter/mqpar.xml" + } + 'openms' { + idxml1 = "${params.nf_core_test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML" + idxml2 = "${params.nf_core_test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML" + } + 'pdb' { + tim1_pdb = "${params.nf_core_test_data_base}/data/proteomics/pdb/1tim.pdb" + tim8_pdb = "${params.nf_core_test_data_base}/data/proteomics/pdb/8tim.pdb" + } + } + 'galaxea_fascicularis' { + hic { + pretext = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext" + } + } + 'deilephila_porcellus' { + 'mito' { + ref_fa = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta" + ref_gb = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb" + hifi_reads = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa" + contigs = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa" + } + } + 'arabidopsis_thaliana' { + 'plastid' { + hifi_reads = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta" + } + } + + 'imaging' { + 'h5' { + plant_wga = "${params.nf_core_test_data_base}/data/imaging/h5/plant_wga.h5" + plant_wga_prob = "${params.nf_core_test_data_base}/data/imaging/h5/plant_wga_probabilities.h5" + } + 'ilp' { + plant_wga_multicut = "${params.nf_core_test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp" + plant_wga_pixel_class = "${params.nf_core_test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp" + } + 'tiff' { + mouse_heart_wga = "${params.nf_core_test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff" + } + 'ome-tiff' { + cycif_tonsil_channels = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv" + cycif_tonsil_cycle1 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycif_tonsil_cycle2 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + cycif_tonsil_cycle3 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif" + cycif_tonsil_dfp = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif" + cycif_tonsil_ffp = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif" + } + 'registration' { + markers = "${params.nf_core_test_data_base}/data/imaging/registration/markers.csv" + cycle1 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycle2 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + } + 'segmentation' { + markers = "${params.nf_core_test_data_base}/data/imaging/segmentation/markers.csv" + image = "${params.nf_core_test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif" + } + 'quantification' { + markers = "${params.nf_core_test_data_base}/data/imaging/quantification/markers.csv" + image = "${params.nf_core_test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif" + mask = "${params.nf_core_test_data_base}/data/imaging/quantification/cell.ome.tif" + } + 'downstream' { + markers = "${params.nf_core_test_data_base}/data/imaging/downstream/markers.csv" + cell_feature_array = "${params.nf_core_test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv" + } + 'background_subtraction' { + markers = "${params.nf_core_test_data_base}/data/imaging/background_subtraction/markers.csv" + image = "${params.nf_core_test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif" + } + 'core_detection' { + image = "${params.nf_core_test_data_base}/data/imaging/core_detection/single_core_dapi.tif" } } } diff --git a/modules.json b/modules.json index 398d08e..cbe3a35 100644 --- a/modules.json +++ b/modules.json @@ -112,6 +112,16 @@ "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] }, + "pharokka/installdatabases": { + "branch": "master", + "git_sha": "10e88ef2f1f3ff012a2c9562de95c264006ebf21", + "installed_by": ["modules"] + }, + "pharokka/pharokka": { + "branch": "master", + "git_sha": "10e88ef2f1f3ff012a2c9562de95c264006ebf21", + "installed_by": ["modules"] + }, "samtools/flagstat": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", diff --git a/modules/local/prodigal/prodigalgv/main.nf b/modules/local/prodigal/prodigalgv/main.nf index c95d5cf..29bf06c 100644 --- a/modules/local/prodigal/prodigalgv/main.nf +++ b/modules/local/prodigal/prodigalgv/main.nf @@ -44,6 +44,8 @@ process PRODIGAL_PRODIGALGV { touch ${prefix}.prodigalgv.fna touch ${prefix}.prodigalgv.faa + gzip ${prefix}.prodigalgv.faa ${prefix}.prodigalgv.fna + cat <<-END_VERSIONS > versions.yml "${task.process}": prodigalgv: \$(echo \$(prodigal-gv --version 2>&1) | awk 'NF{ print \$NF }') diff --git a/modules/local/prodigal/prodigalgv/tests/main.nf.test b/modules/local/prodigal/prodigalgv/tests/main.nf.test index cc4119d..35c1748 100644 --- a/modules/local/prodigal/prodigalgv/tests/main.nf.test +++ b/modules/local/prodigal/prodigalgv/tests/main.nf.test @@ -5,6 +5,7 @@ nextflow_process { process "PRODIGAL_PRODIGALGV" tag "modules" tag "modules_local" + tag "prodigal" tag "prodigal/prodigalgv" diff --git a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap b/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap index 2129402..c441b57 100644 --- a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap +++ b/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap @@ -42,6 +42,6 @@ ] } ], - "timestamp": "2023-12-06T15:25:14.501666251" + "timestamp": "2024-01-24T09:50:38.063764149" } } \ No newline at end of file diff --git a/modules/nf-core/mash/screen/nextflow.config b/modules/nf-core/mash/screen/nextflow.config index fe224be..4471867 100644 --- a/modules/nf-core/mash/screen/nextflow.config +++ b/modules/nf-core/mash/screen/nextflow.config @@ -1,6 +1,5 @@ process { withName: MASH_SCREEN { - ext.args = params.mash_screen_min_score ? "-i ${params.mash_screen_min_score}" : "" ext.args = [ params.mash_screen_min_score ? "-i ${params.mash_screen_min_score}" : "", params.mash_screen_winner_take_all ? "-w" : "", diff --git a/modules/nf-core/pharokka/installdatabases/environment.yml b/modules/nf-core/pharokka/installdatabases/environment.yml new file mode 100644 index 0000000..5a9ea8f --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "pharokka_installdatabases" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::pharokka=1.5.1" diff --git a/modules/nf-core/pharokka/installdatabases/main.nf b/modules/nf-core/pharokka/installdatabases/main.nf new file mode 100644 index 0000000..7adf70c --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/main.nf @@ -0,0 +1,81 @@ +process PHAROKKA_INSTALLDATABASES { + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pharokka:1.5.1--pyhdfd78af_0': + 'biocontainers/pharokka:1.5.1--pyhdfd78af_0' }" + + output: + path("${prefix}/") , emit: pharokka_db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: 'pharokka_db' + """ + install_databases.py \\ + --outdir $prefix \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pharokka: \$(pharokka.py --version) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: 'pharokka_db' + """ + mkdir -p $prefix + touch $prefix/1Aug2023_data.tsv + touch $prefix/1Aug2023_genomes.fa.msh + touch $prefix/CARD + touch $prefix/CARD.dbtype + touch $prefix/CARD.index + touch $prefix/CARD.lookup + touch $prefix/CARD.source + touch $prefix/CARD_h + touch $prefix/CARD_h.dbtype + touch $prefix/CARD_h.index + touch $prefix/VFDB_setB_pro.fas.gz + touch $prefix/VFDBclusterRes_cluster.tsv + touch $prefix/VFDBclusterRes_rep_seq.fasta + touch $prefix/all_phrogs.h3m + touch $prefix/aro_index.tsv + touch $prefix/phrog_annot_v4.tsv + touch $prefix/phrogs_db + touch $prefix/phrogs_db.dbtype + touch $prefix/phrogs_db.index + touch $prefix/phrogs_profile_db + touch $prefix/phrogs_profile_db.dbtype + touch $prefix/phrogs_profile_db.index + touch $prefix/phrogs_profile_db_consensus + touch $prefix/phrogs_profile_db_consensus.dbtype + touch $prefix/phrogs_profile_db_consensus.index: + touch $prefix/phrogs_profile_db_h + touch $prefix/phrogs_profile_db_h.index + touch $prefix/phrogs_profile_db_seq + touch $prefix/phrogs_profile_db_seq.dbtype + touch $prefix/phrogs_profile_db_seq.index + touch $prefix/phrogs_profile_db_seq_h + touch $prefix/phrogs_profile_db_seq_h.index + touch $prefix/vfdb + touch $prefix/vfdb.dbtype + touch $prefix/vfdb.index + touch $prefix/vfdb.lookup + touch $prefix/vfdb.source + touch $prefix/vfdb_h + touch $prefix/vfdb_h.dbtype + touch $prefix/vfdb_h.index + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pharokka: \$(pharokka.py --version) + END_VERSIONS + """ +} diff --git a/modules/nf-core/pharokka/installdatabases/meta.yml b/modules/nf-core/pharokka/installdatabases/meta.yml new file mode 100644 index 0000000..a4d0f63 --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/meta.yml @@ -0,0 +1,34 @@ +name: "pharokka_installdatabases" +description: Install databases necessary for Pharokka's functional analysis +keywords: + - pharokka + - prokka + - bakta + - phage + - function + - install + - database + +tools: + - "pharokka": + description: "Fast Phage Annotation Program" + homepage: "https://pharokka.readthedocs.io" + documentation: "https://pharokka.readthedocs.io" + tool_dev_url: "https://github.com/gbouras13/pharokka" + doi: "10.1093/bioinformatics/btac776" + licence: ["MIT"] + +output: + - pharokka_db: + type: directory + description: Directory pointing to Pharokka's database + pattern: "${prefix}/" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@CarsonJM" +maintainers: + - "@CarsonJM" diff --git a/modules/nf-core/pharokka/installdatabases/nextflow.config b/modules/nf-core/pharokka/installdatabases/nextflow.config new file mode 100644 index 0000000..f060329 --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/nextflow.config @@ -0,0 +1,3 @@ +process { + +} \ No newline at end of file diff --git a/modules/nf-core/pharokka/installdatabases/tests/main.nf.test b/modules/nf-core/pharokka/installdatabases/tests/main.nf.test new file mode 100644 index 0000000..040dd85 --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/tests/main.nf.test @@ -0,0 +1,22 @@ +nextflow_process { + + name "Test Process PHAROKKA_INSTALLDATABASES" + script "../main.nf" + process "PHAROKKA_INSTALLDATABASES" + + tag "modules" + tag "modules_nfcore" + tag "pharokka" + tag "pharokka/installdatabases" + + test("No input required") { + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/pharokka/installdatabases/tests/main.nf.test.snap b/modules/nf-core/pharokka/installdatabases/tests/main.nf.test.snap new file mode 100644 index 0000000..04d4c2a --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/tests/main.nf.test.snap @@ -0,0 +1,103 @@ +{ + "No input required": { + "content": [ + { + "0": [ + [ + "1Aug2023_data.tsv:md5,5c353dc3302ee99b477f94463c91ac22", + "1Aug2023_genomes.fa.msh:md5,90a1d0e96e075fdf85873d9fef58ca11", + "CARD:md5,61734c072e5202a8e7ec97c963283122", + "CARD.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "CARD.index:md5,97c1d480c91c784ec9799375644c128a", + "CARD.lookup:md5,00b9f03eae491f5c55b0c4d5c41e5a7e", + "CARD.source:md5,eece777623b8779e0c1bdb3b026dff86", + "CARD_h:md5,079ea8c12462920077f821dd8a9f5005", + "CARD_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "CARD_h.index:md5,ffaccf1b30a31f716b1a5abddfb507e4", + "VFDB_setB_pro.fas.gz:md5,64ef8e83740cc54f9ca24a02421e4192", + "VFDBclusterRes_cluster.tsv:md5,dc54c0984378d4be7441fbf67c9c102d", + "VFDBclusterRes_rep_seq.fasta:md5,a7b5569129d71a8a98b742c82fb2570c", + "all_phrogs.h3m:md5,602dbaa02a49809a2861c2406184eeb1", + "aro_index.tsv:md5,80af719eb74cc11e1c36ccc2abc39ab0", + "phrog_annot_v4.tsv:md5,3f078c589efeef3352c5e60c1ced9a44", + "phrogs_db:md5,75649b7e711af909288b94ebaec8e724", + "phrogs_db.dbtype:md5,c31b034959815c44d4dafd6f30846159", + "phrogs_db.index:md5,cd1b2517d80797c8e2fb0f6666482a1d", + "phrogs_profile_db:md5,d355c1b2599c9fa1a2e19b587cc3e75a", + "phrogs_profile_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828", + "phrogs_profile_db.index:md5,61d1b0e42f135379b553c8f48372ca44", + "phrogs_profile_db_consensus:md5,4107609c2701b2eca2f561177d1498f3", + "phrogs_profile_db_consensus.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "phrogs_profile_db_consensus.index:md5,a711c8e652b63aa2aceb20716ae8c600", + "phrogs_profile_db_h:md5,25c9cbd7ac212a198f6da1e1883ea5b9", + "phrogs_profile_db_h.index:md5,ae5e93f21c408190ea41e1bbf1b10ff4", + "phrogs_profile_db_seq:md5,566a77a95040aeed03d72f2d7a369607", + "phrogs_profile_db_seq.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "phrogs_profile_db_seq.index:md5,a711c8e652b63aa2aceb20716ae8c600", + "phrogs_profile_db_seq_h:md5,25c9cbd7ac212a198f6da1e1883ea5b9", + "phrogs_profile_db_seq_h.index:md5,ae5e93f21c408190ea41e1bbf1b10ff4", + "vfdb:md5,446b970439c75b0badb040d65f38b35a", + "vfdb.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "vfdb.index:md5,7f2db97d9249bc732d959c624d0d6b53", + "vfdb.lookup:md5,64b6b736ca97b383b166d39d7008db34", + "vfdb.source:md5,9bd8ca6ad5c3d7dd3608b78efdb78500", + "vfdb_h:md5,c7fdb80aa827a262cf8132ebdb940239", + "vfdb_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "vfdb_h.index:md5,b8a30c4893ee24771368bb3cdbe8e179" + ] + ], + "1": [ + "versions.yml:md5,6a73f19a3abede8c77921502c9455488" + ], + "pharokka_db": [ + [ + "1Aug2023_data.tsv:md5,5c353dc3302ee99b477f94463c91ac22", + "1Aug2023_genomes.fa.msh:md5,90a1d0e96e075fdf85873d9fef58ca11", + "CARD:md5,61734c072e5202a8e7ec97c963283122", + "CARD.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "CARD.index:md5,97c1d480c91c784ec9799375644c128a", + "CARD.lookup:md5,00b9f03eae491f5c55b0c4d5c41e5a7e", + "CARD.source:md5,eece777623b8779e0c1bdb3b026dff86", + "CARD_h:md5,079ea8c12462920077f821dd8a9f5005", + "CARD_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "CARD_h.index:md5,ffaccf1b30a31f716b1a5abddfb507e4", + "VFDB_setB_pro.fas.gz:md5,64ef8e83740cc54f9ca24a02421e4192", + "VFDBclusterRes_cluster.tsv:md5,dc54c0984378d4be7441fbf67c9c102d", + "VFDBclusterRes_rep_seq.fasta:md5,a7b5569129d71a8a98b742c82fb2570c", + "all_phrogs.h3m:md5,602dbaa02a49809a2861c2406184eeb1", + "aro_index.tsv:md5,80af719eb74cc11e1c36ccc2abc39ab0", + "phrog_annot_v4.tsv:md5,3f078c589efeef3352c5e60c1ced9a44", + "phrogs_db:md5,75649b7e711af909288b94ebaec8e724", + "phrogs_db.dbtype:md5,c31b034959815c44d4dafd6f30846159", + "phrogs_db.index:md5,cd1b2517d80797c8e2fb0f6666482a1d", + "phrogs_profile_db:md5,d355c1b2599c9fa1a2e19b587cc3e75a", + "phrogs_profile_db.dbtype:md5,f2dd0dedb2c260419ece4a9e03b2e828", + "phrogs_profile_db.index:md5,61d1b0e42f135379b553c8f48372ca44", + "phrogs_profile_db_consensus:md5,4107609c2701b2eca2f561177d1498f3", + "phrogs_profile_db_consensus.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "phrogs_profile_db_consensus.index:md5,a711c8e652b63aa2aceb20716ae8c600", + "phrogs_profile_db_h:md5,25c9cbd7ac212a198f6da1e1883ea5b9", + "phrogs_profile_db_h.index:md5,ae5e93f21c408190ea41e1bbf1b10ff4", + "phrogs_profile_db_seq:md5,566a77a95040aeed03d72f2d7a369607", + "phrogs_profile_db_seq.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "phrogs_profile_db_seq.index:md5,a711c8e652b63aa2aceb20716ae8c600", + "phrogs_profile_db_seq_h:md5,25c9cbd7ac212a198f6da1e1883ea5b9", + "phrogs_profile_db_seq_h.index:md5,ae5e93f21c408190ea41e1bbf1b10ff4", + "vfdb:md5,446b970439c75b0badb040d65f38b35a", + "vfdb.dbtype:md5,f1d3ff8443297732862df21dc4e57262", + "vfdb.index:md5,7f2db97d9249bc732d959c624d0d6b53", + "vfdb.lookup:md5,64b6b736ca97b383b166d39d7008db34", + "vfdb.source:md5,9bd8ca6ad5c3d7dd3608b78efdb78500", + "vfdb_h:md5,c7fdb80aa827a262cf8132ebdb940239", + "vfdb_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2", + "vfdb_h.index:md5,b8a30c4893ee24771368bb3cdbe8e179" + ] + ], + "versions": [ + "versions.yml:md5,6a73f19a3abede8c77921502c9455488" + ] + } + ], + "timestamp": "2023-12-15T20:01:50.473933189" + } +} \ No newline at end of file diff --git a/modules/nf-core/pharokka/installdatabases/tests/tags.yml b/modules/nf-core/pharokka/installdatabases/tests/tags.yml new file mode 100644 index 0000000..cace088 --- /dev/null +++ b/modules/nf-core/pharokka/installdatabases/tests/tags.yml @@ -0,0 +1,2 @@ +pharokka/installdatabases: + - "modules/nf-core/pharokka/installdatabases/**" diff --git a/modules/nf-core/pharokka/pharokka/environment.yml b/modules/nf-core/pharokka/pharokka/environment.yml new file mode 100644 index 0000000..7e6edda --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "pharokka_pharokka" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::pharokka=1.5.1" diff --git a/modules/nf-core/pharokka/pharokka/main.nf b/modules/nf-core/pharokka/pharokka/main.nf new file mode 100644 index 0000000..677e331 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/main.nf @@ -0,0 +1,68 @@ +process PHAROKKA_PHAROKKA { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pharokka:1.5.1--pyhdfd78af_0': + 'biocontainers/pharokka:1.5.1--pyhdfd78af_0' }" + + input: + tuple val(meta), path(phage_fasta) + path pharokka_db + + output: + tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv") , emit: cds_final_merged_output + tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_functions.tsv") , emit: cds_functions + tuple val(meta), path("${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv") , emit: length_gc_cds_density + tuple val(meta), path("${prefix}_pharokka/p*.ffn.gz") , emit: ffn + tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_card.tsv") , emit: card , optional: true + tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv") , emit: vfdb , optional: true + tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv") , emit: mash , optional: true + tuple val(meta), path("${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta.gz") , emit: reoriented , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + """ + pharokka.py \\ + --infile ${phage_fasta} \\ + --outdir ${prefix}_pharokka \\ + --database ${pharokka_db} \\ + --threads ${task.cpus} \\ + --prefix ${prefix} \\ + $args + + gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pharokka: \$(pharokka.py --version) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + """ + mkdir -p ${prefix}_pharokka + touch ${prefix}_pharokka/${prefix}.gbk + touch ${prefix}_pharokka/${prefix}.log + touch ${prefix}_pharokka/${prefix}_cds_functions.tsv + touch ${prefix}_pharokka/${prefix}_top_hits_card.tsv + touch ${prefix}_pharokka/top_hits_vfdb.tsv + touch ${prefix}_pharokka/${prefix}_top_hits_inphared + touch ${prefix}_pharokka/${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pharokka: \$(pharokka.py --version) + END_VERSIONS + """ +} diff --git a/modules/nf-core/pharokka/pharokka/meta.yml b/modules/nf-core/pharokka/pharokka/meta.yml new file mode 100644 index 0000000..fbba281 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/meta.yml @@ -0,0 +1,71 @@ +name: "pharokka_pharokka" +description: Functional annotation of phages +keywords: + - pharokka + - phage + - function + - prokka + - bakta + +tools: + - "pharokka": + description: "Fast Phage Annotation Program" + homepage: "https://pharokka.readthedocs.io" + documentation: "https://pharokka.readthedocs.io" + tool_dev_url: "https://github.com/gbouras13/pharokka" + doi: "10.1093/bioinformatics/btac776" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - phage_fasta: + type: file + description: A FASTA file containing phage sequence(s) + pattern: "*.{fasta,fna,fa}" + - pharokka_db: + type: file + description: Directory containing Pharokka's database + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - log: + type: file + description: Log file containing all logging output + pattern: "*.log" + - cds_functions: + type: file + description: A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs + pattern: "*_cds_functions.tsv" + - card: + type: file + description: OPTIONAL - A file containing any CARD database hits + pattern: "*top_hits_card.tsv" + - vfdb: + type: file + description: OPTIONAL - A file containing any VFDB database hits + pattern: "*top_hits_vfdb.tsv" + - mash: + type: file + description: OPTIONAL - File containing top hits to INPHARED database + pattern: "*_top_hits_mash_inphared.tsv" + - reoriented: + type: file + description: OPTIONAL - FASTA file reoriented to start with the large terminase subunit + pattern: "*_genome_terminase_reoriented.fasta" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@CarsonJM" +maintainers: + - "@CarsonJM" diff --git a/modules/nf-core/pharokka/pharokka/nextflow.config b/modules/nf-core/pharokka/pharokka/nextflow.config new file mode 100644 index 0000000..34f3bbe --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/nextflow.config @@ -0,0 +1,12 @@ +process { + withName: PHAROKKA_PHAROKKA { + ext.args = [ + "--genbank --meta", + ].join(' ').trim() + publishDir = [ + path: { "${params.outdir}/PhageFunction/pharokka/pharokka" }, + mode: params.publish_dir_mode, + pattern: '*', + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/pharokka/pharokka/tests/main.nf.test b/modules/nf-core/pharokka/pharokka/tests/main.nf.test new file mode 100644 index 0000000..83a6f30 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/tests/main.nf.test @@ -0,0 +1,46 @@ +nextflow_process { + + name "Test Process PHAROKKA_PHAROKKA" + script "../main.nf" + process "PHAROKKA_PHAROKKA" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "pharokka" + tag "pharokka/pharokka" + tag "pharokka/installdatabases" + + test("sarscov2 - genome - fasta") { + setup { + run("PHAROKKA_INSTALLDATABASES") { + script "../../installdatabases/main.nf" + } + } + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + input[1] = PHAROKKA_INSTALLDATABASES.out.pharokka_db + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.cds_functions, + process.out.length_gc_cds_density, + process.out.versions + ).match() + }, + { assert file(process.out.cds_final_merged_output[0][1]).exists() } + ) + } + } +} diff --git a/modules/nf-core/pharokka/pharokka/tests/main.nf.test.snap b/modules/nf-core/pharokka/pharokka/tests/main.nf.test.snap new file mode 100644 index 0000000..0d07b92 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "sarscov2 - genome - fasta": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_cds_functions.tsv:md5,ba4bd022017c08732cc0d4605c6d3239" + ] + ], + [ + [ + { + "id": "test" + }, + "test_length_gc_cds_density.tsv:md5,cb1748de2145255ff21ede8047d727fe" + ] + ], + [ + "versions.yml:md5,6b7daa5df4b6038456d3c81f0cb4f960" + ] + ], + "timestamp": "2023-12-27T21:20:12.003909628" + } +} \ No newline at end of file diff --git a/modules/nf-core/pharokka/pharokka/tests/nextflow.config b/modules/nf-core/pharokka/pharokka/tests/nextflow.config new file mode 100644 index 0000000..6025ecf --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: PHAROKKA_PHAROKKA { + ext.args = [ + "--fast --skip_extra_annotations --skip_mash" + ].join(' ').trim() + } +} + diff --git a/modules/nf-core/pharokka/pharokka/tests/tags.yml b/modules/nf-core/pharokka/pharokka/tests/tags.yml new file mode 100644 index 0000000..1a161f5 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/tests/tags.yml @@ -0,0 +1,2 @@ +pharokka/pharokka: + - "modules/nf-core/pharokka/pharokka/**" diff --git a/nextflow.config b/nextflow.config index 0044d9b..3ef9317 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,8 +71,9 @@ params { // Phage lifestyle options skip_bacphlip = false - // Virus ORF calling - skip_prodigalgv = false + // Phage functional annotation + skip_pharokka = false + pharokka_db = null // Virus microdiversity options skip_instrain = false @@ -243,9 +244,11 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } - test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config' } - nf_test { includeConfig 'nf_test.config' } + test { + includeConfig 'conf/test.config' + includeConfig 'conf/test_data.config' + } + test_full { includeConfig 'conf/test_full.config' } } // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile diff --git a/subworkflows/local/fasta_microdiversity_instrain/main.nf b/subworkflows/local/fasta_microdiversity_instrain/main.nf index 21060fa..7516b99 100644 --- a/subworkflows/local/fasta_microdiversity_instrain/main.nf +++ b/subworkflows/local/fasta_microdiversity_instrain/main.nf @@ -2,8 +2,6 @@ // Assess virus microdiversity with instrain // -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_PROTEINS } from '../../../modules/nf-core/gunzip/main' include { INSTRAIN_PROFILE } from '../../../modules/nf-core/instrain/profile/main' include { INSTRAIN_COMPARE } from '../../../modules/nf-core/instrain/compare/main' @@ -11,33 +9,22 @@ include { INSTRAIN_COMPARE } from '../../../modules/nf-core/instrain/co workflow FASTA_MICRODIVERSITY_INSTRAIN { take: bam // [ [ meta ], bam ] , BAM files from reads aligned to FASTA file (mandatory) - fasta_gz // [ [ meta ], fasta.gz ] , FASTA file used in read alignment (mandatory) - proteins_fna_gz // [ [ meta ], fna.gz ] , FASTA file for protein-coding genes (optional) + genome_fasta // [ [ meta ], fasta ] , FASTA file used in read alignment (mandatory) + proteins_fna // [ [ meta ], fna ] , FASTA file for protein-coding genes (optional) instrain_stb // [ [ meta ], stb.tsv ] , TSV file with two columns for associationg scaffolds to bins (optional) main: ch_versions = Channel.empty() - // - // MODULE: gunzip FASTA file - // - fasta = GUNZIP_FASTA ( fasta_gz ).gunzip - - // - // MODULE: gunzip proteins fna file - // - proteins_fna = GUNZIP_PROTEINS ( proteins_fna_gz ).gunzip - ch_versions = ch_versions.mix(GUNZIP_PROTEINS.out.versions) - // remove meta information for instrain profile inputs ch_stb_file_tsv_nometa = instrain_stb.map { it[1] }.first() - ch_fasta_nometa = fasta.map { it[1] }.first() + ch_genome_fasta_nometa = genome_fasta.map { it[1] }.first() ch_proteins_fna_nometa = proteins_fna.map { it[1] }.first() // // MODULE: Profile microdiveristy within each sample // - ch_instrain_profiles = INSTRAIN_PROFILE ( bam, ch_fasta_nometa, ch_proteins_fna_nometa, ch_stb_file_tsv_nometa ).profile + ch_instrain_profiles = INSTRAIN_PROFILE ( bam, ch_genome_fasta_nometa, ch_proteins_fna_nometa, ch_stb_file_tsv_nometa ).profile ch_instrain_gene_tsv = INSTRAIN_PROFILE.out.gene_info ch_versions = ch_versions.mix(INSTRAIN_PROFILE.out.versions) diff --git a/subworkflows/local/fasta_phage_function_pharokka/main.nf b/subworkflows/local/fasta_phage_function_pharokka/main.nf new file mode 100644 index 0000000..d25dec8 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/main.nf @@ -0,0 +1,38 @@ +// +// Functionally annotate phage sequences using Pharokka +// + +include { PHAROKKA_INSTALLDATABASES } from '../../../modules/nf-core/pharokka/installdatabases/main' +include { PHAROKKA_PHAROKKA } from '../../../modules/nf-core/pharokka/pharokka/main' + +workflow FASTA_PHAGE_FUNCTION_PHAROKKA { + take: + virus_fasta // [ [ meta ], fasta ] , virus sequences (mandatory) + pharokka_db // [ pharokka_db ] , Pharokka database directory (optional) + + main: + ch_versions = Channel.empty() + + // if pharokka_db exists, skip database download + if ( pharokka_db ){ + ch_pharokka_db = pharokka_db + } else { + // + // MODULE: download standard pharokka database + // + ch_pharokka_db = PHAROKKA_INSTALLDATABASES( ).pharokka_db + ch_versions = ch_versions.mix(PHAROKKA_INSTALLDATABASES.out.versions) + } + + // + // MODULE: Functionally annotate phages + // + ch_pharokka_ffn_gz = PHAROKKA_PHAROKKA ( virus_fasta, ch_pharokka_db ).ffn + pharokka_final_output_tsv = PHAROKKA_PHAROKKA.out.cds_final_merged_output + ch_versions = ch_versions.mix(PHAROKKA_PHAROKKA.out.versions.first()) + + emit: + versions = ch_versions // [ versions.yml ] + pharokka_ffn_gz = ch_pharokka_ffn_gz // [ [ meta ], ffn.gz ] + pharokka_final_output_tsv = pharokka_final_output_tsv // [ [ meta ], tsv ] +} diff --git a/subworkflows/local/fasta_phage_function_pharokka/nextflow.config b/subworkflows/local/fasta_phage_function_pharokka/nextflow.config new file mode 100644 index 0000000..59eb679 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/nextflow.config @@ -0,0 +1,2 @@ +includeConfig '../../../modules/nf-core/pharokka/installdatabases/nextflow.config' +includeConfig '../../../modules/nf-core/pharokka/pharokka/nextflow.config' diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test new file mode 100644 index 0000000..4452610 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_workflow { + + name "Test Subworkflow: FASTA_PHAGE_FUNCTION_PHAROKKA" + script "../main.nf" + workflow "FASTA_PHAGE_FUNCTION_PHAROKKA" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_local" + tag "fasta_phage_function_pharokka" + tag "fasta_phage_function_pharokka_default" + + + test("Parameters: default") { + + when { + workflow { + """ + input[0] = Channel.of([ [ id:'test' ], [ params.test_data['sarscov2']['genome']['genome_fasta'] ] ]) + input[1] = null + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap new file mode 100644 index 0000000..83b6c12 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Parameters: default": { + "content": [ + { + "0": [ + "versions.yml:md5,7715e330cd5621f95141e256b567ec19" + ], + "1": [ + + ], + "2": [ + + ], + "pharokka_ffn_gz": [ + + ], + "pharokka_final_output_tsv": [ + + ], + "versions": [ + "versions.yml:md5,7715e330cd5621f95141e256b567ec19" + ] + } + ], + "timestamp": "2024-01-24T09:28:21.667432563" + } +} \ No newline at end of file diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config b/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config new file mode 100644 index 0000000..4fdbc96 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: PHAROKKA_PHAROKKA { + ext.args = "--locustag TEST --meta" + } +} diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/pharokka_db_provided.test b/subworkflows/local/fasta_phage_function_pharokka/tests/pharokka_db_provided.test new file mode 100644 index 0000000..07fc0f0 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/pharokka_db_provided.test @@ -0,0 +1,34 @@ +nextflow_workflow { + + name "Test Subworkflow: FASTA_PHAGE_FUNCTION_PHAROKKA" + script "../main.nf" + workflow "FASTA_PHAGE_FUNCTION_PHAROKKA" + tag "subworkflows" + tag "subworkflows_local" + tag "fasta_phage_function_pharokka" + tag "fasta_phage_function_pharokka_db_provided" + + + test("Parameters: --pharokka_db provided") { + + when { + params { + load("$baseDir/tests/nf-test-local-db-params.json") + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ [ id:'test' ], [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]) + input[1] = Channel.of([ file(params.pharokka_db, checkIfExists:true ) ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/tags.yml b/subworkflows/local/fasta_phage_function_pharokka/tests/tags.yml new file mode 100644 index 0000000..a3485b8 --- /dev/null +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/tags.yml @@ -0,0 +1,2 @@ +fasta_phage_function_pharokka_default: + - subworkflows/local/fasta_phage_function_pharokka/** diff --git a/subworkflows/local/fasta_phage_host_iphop/main.nf b/subworkflows/local/fasta_phage_host_iphop/main.nf index 4a7d2de..91f6059 100644 --- a/subworkflows/local/fasta_phage_host_iphop/main.nf +++ b/subworkflows/local/fasta_phage_host_iphop/main.nf @@ -5,13 +5,12 @@ include { IPHOP_DOWNLOAD } from '../../../modules/nf-core/iphop/download/main' include { UNTAR } from '../../../modules/nf-core/untar/main' include { UNTAR as UNTAR2 } from '../../../modules/nf-core/untar/main' -include { GUNZIP } from '../../../modules/nf-core/gunzip/main' include { IPHOP_PREDICT } from '../../../modules/nf-core/iphop/predict/main' workflow FASTA_PHAGE_HOST_IPHOP { take: - virus_fasta_gz // [ [ meta ], fasta.gz ] , virus sequences (mandatory) - iphop_db // [ checkv_db ] , iPHoP database directory (optional) + virus_fasta // [ [ meta ], fasta ] , virus sequences (mandatory) + iphop_db // [ checkv_db ] , iPHoP database directory (optional) main: ch_versions = Channel.empty() @@ -36,12 +35,6 @@ workflow FASTA_PHAGE_HOST_IPHOP { } } - // - // MODULE: Gunzip fasta for IPHoP - // - ch_viruses_fasta = GUNZIP ( virus_fasta_gz ).gunzip - ch_versions = ch_versions.mix(GUNZIP.out.versions.first()) - // create input for partial iphop run ch_iphop_partial_input = [] if ( params.iphop_partial_test ) { @@ -55,11 +48,10 @@ workflow FASTA_PHAGE_HOST_IPHOP { // // MODULE: Predict virus host // - IPHOP_PREDICT ( ch_viruses_fasta, ch_iphop_db, ch_iphop_partial_input ) - ch_host_predictions_tsv = IPHOP_PREDICT.out.iphop_genus + ch_host_predictions_tsv = IPHOP_PREDICT ( virus_fasta, ch_iphop_db, ch_iphop_partial_input ).iphop_genus ch_versions = ch_versions.mix(IPHOP_PREDICT.out.versions.first()) emit: - host_predictions_tsv = ch_host_predictions_tsv // [ [ meta ], genus_predictions.tsv ] , TSV file containing host genus predictions + host_predictions_tsv = ch_host_predictions_tsv // [ [ meta ], genus_predictions.tsv ] , TSV file containing host genus predictions versions = ch_versions // [ versions.yml ] } diff --git a/subworkflows/local/fasta_virus_quality_checkv/main.nf b/subworkflows/local/fasta_virus_quality_checkv/main.nf index cdd9c4d..16c4adf 100644 --- a/subworkflows/local/fasta_virus_quality_checkv/main.nf +++ b/subworkflows/local/fasta_virus_quality_checkv/main.nf @@ -4,7 +4,6 @@ include { CHECKV_DOWNLOADDATABASE } from '../../../modules/nf-core/checkv/downloaddatabase/main' include { UNTAR } from '../../../modules/nf-core/untar/main' -include { GUNZIP } from '../../../modules/nf-core/gunzip/main' include { CHECKV_ENDTOEND } from '../../../modules/nf-core/checkv/endtoend/main' // TODO: Update nf-core module to gzip output FASTA files workflow FASTA_VIRUS_QUALITY_CHECKV { @@ -35,12 +34,6 @@ workflow FASTA_VIRUS_QUALITY_CHECKV { } } - // - // MODULE: Gunzip fasta for checkV - // - ch_viruses_fasta = GUNZIP ( virus_fasta_gz ).gunzip - ch_versions = ch_versions.mix(GUNZIP.out.versions.first()) - // // MODULE: Assess virus quality // diff --git a/test.faa b/test.faa new file mode 100644 index 0000000..4053a09 --- /dev/null +++ b/test.faa @@ -0,0 +1,101 @@ +>chr22_1 # 4575 # 4697 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.398 +MEKLINLTDIVKQEKKDETQKLCDSSLCLRLFSLQWGRVV* +>chr22_2 # 5954 # 6520 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=TTA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.337 +MSKTSLKYFSLKITCGVNRLWCFYYLKTTFILQMFLRRGECEGRGQNREEFEWITFFISI +LLIWGMSLREGWKLWEYIVYRKRINSSSWMGLWRLNCKSQHWQHPQLIILGDRIIQLGCF +ININNTIFNYYIKNFKYIYVPWPGKPVFYFHKNYFYCMKRLWGLAQNICGPDKIGLVTLP +QKENGKKK* +>chr22_3 # 8336 # 8563 # -1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=TTAA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.298 +MVKEKPTLTFCNVYENWKQNQFACSLTSFLGSDLQMTWKKVHLPIAYTYIHMYVYIHIFL +KIQAYNSLCLKEVNI* +>chr22_4 # 11642 # 11989 # -1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.405 +MLHFIVFKHQFQSDDFCFLFWMQWFLRFQTVCRPLAQYLKYLMDMVINLKLFWKKSPADR +APFSTGSVSQEPKSRWGSLSVSLEQKPQRAFLQGNILLQEIKTETTEALLGVESS* +>chr22_5 # 12499 # 12948 # -1 # ID=1_5;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.464 +MAHACNPSTLGGQGGWITWGQELETSLANTLSLLKIQKLAGHGSWAPVIPANCVHKLITA +PKCRTKFSSKWRTFFFFSNWSIRREESTCTAIHTDIMDDWLDCAFTCGVHCRGHGKYSCL +RVFVNLTHSAQKALLHYNEEAVQINPKVL* +>chr22_6 # 13971 # 14360 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=TTAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.454 +MSSASCVHRPQNPSIPESPFPTVAAPLLAGTPSSGLVFPLQKRTRSANLRLPYADAKYYV +SYFIPSQSFWLQTSFYFNFITIGFFLMLLLLFVCFFWDRVFLCHLGWSKVAQSQLTATSA +SRVQAILLP* +>chr22_7 # 14374 # 14874 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.477 +MQHMFEKQFYTVDRVEKMALWKFSSNSQNAPAGKVDPGKFRGHMPLYSEKYFLSFFFFFR +WSLPLSPRLECTGAISAHCKLRLPGSRHSPASAARVTGITGLRHHAWLTFCIFSRDGRGF +TVLARMVSISWPHDPPASASQSTGITDVSHCARLKNIFISSSTFIS* +>chr22_8 # 16449 # 16853 # -1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=AATAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.420 +MVVNTCSPSYWGAEVEGFLEPRKSRLQWAVIGPLHSSLGDKVRPFLKKKKKKDFNLQKHW +SSDEEKKVSIPNCEKNCEETIENKTTEKSCHSLPVLSLHGPASSHVYWVVSPESLFIYLF +IFEMESCSVTQAGV* +>chr22_9 # 17198 # 17380 # 1 # ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.492 +MTGLRIAQMDEQFPRLIPSLHYPSQPLISFISQDLVLIFLPCFLRIVAIVPWLLDQPGAQ +* +>chr22_10 # 18024 # 18590 # -1 # ID=1_10;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.519 +MAWSWLTASTSRVQVILLPQPPSSWDYRGPPLSQTNFIYLFIYFLRWHLTLSPSLECSGV +ISAHCNLHLPGSRDSSVSASWVAGTTGVRHHARIIFVFLVETGSHHNGQAGLELLTSWST +HLSLPKCWDYRHEPLPPANFFEFFVETGFHHVGQAGLEPLTSNDSPASTSQSAGITGMNH +RPQHKCPL* +>chr22_11 # 20113 # 20742 # -1 # ID=1_11;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.459 +MRLVPFQFSTFFVFFFWETESCSVAQAGVQWRDLGSLQPPPPRFKRFSCLSLLNSWDYRC +APPRPAIFCIFSRDGVSPYWPGWSRTPDLMILPPQPPKVLGLQARATVPSQFLTFSFCVS +IRCSSFPMIRAGFNSIKIFKLSTYVGFGRAKHSAAISSQLFEHSLHDILTYMDLCLDVTL +GVWKHQLQLTRVVSPSCCGYLKKKKGLSS* +>chr22_12 # 20878 # 22551 # -1 # ID=1_12;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.568 +MDSTVPSALELPQRLALNPRESPRSPEEEEPHLLSSLAAVQTLASVIRPCYGPHGRQKFL +VTMKGETVCTGCATAILRALELEHPAAWLLREAGQTQAENSGDGTAFVVLLTEALLEQAE +QLLKAGLPRPQLREAYATATAEVLATLPSLAIQSLGPLEDPSWALHSVMNTHTLSPMDHL +TKLVAHACWAIKELDGSFKPERVGVCALPGGTLEDSCLLPGLAISGKLCGQMATVLSGAR +VALFACPFGPAHPNAPATARLSSPADLAQFSKGSDQLLEKQVGQLAAAGINVAVVLGEVD +EETLTLADKYGIVVIQARSWMEIIYLSEVLDTPLLPRLLPPQRPGKCQRVYRQELGDGLA +VVFEWECTGTPALTVVLRGATTQGLRSAEQAVYHGIDAYFQLCQDPRLIPGAGATEMALA +KMLSDKGSRLEGPSGPAFLAFAWALKYLPKTLAENAGLAVSDVMAEMSGVHQGGNLLMGV +GTEGIINVAQEGVWDTLIVKAQGFRAVAEVVLQLVTVDEIVVAKKSPTHQEIWNPDSKKT +KKHPPPVETKKILGLNN* +>chr22_13 # 23191 # 23703 # 1 # ID=1_13;partial=00;start_type=GTG;rbs_motif=TTTTA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.489 +MFLSVVQAGLEFLASREPSTLASQSARTTGVSHHLTHPFFFFFFETESHSVAQAGVQWYN +LSSLQPPPPRFKQFSCLSLSVAGITGASHHARLIFYIFSRDRGISPCWPWLARLVSNSWP +QVIRPPRPPKVLGLQVWATAPGLFFLFEKELRDDVCVLFCFGVTFSCSTV* +>chr22_14 # 25201 # 25689 # 1 # ID=1_14;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.474 +MLNQCTICKVAHSLSFSAISCGFFKLLSQGTRKLCCFQSALSFYGEVFAITSDDTIWLGH +CAHFLQSYFLLAPSCIHQSLRCPPGAIFLPAAELWPWWVQGGWCAEQGLRRRGSVLSRNV +SKEILFGLRTMNDYFEHFWFWRLHLDQAWSSKFRLLKACTSE* +>chr22_15 # 25895 # 26122 # -1 # ID=1_15;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.443 +MPELHLAQASQSAGIIGSSHGHWPVVFILFIYLFIYLFIYFLRLSLALLPRLEYSGAILA +HCNLSTSQVQEILVP* +>chr22_16 # 27925 # 28575 # 1 # ID=1_16;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.524 +MIYFTEITYIAIWIFFLRRSFALVAQARVQWRDLGSLQPPPPGFKQFSCLSLQNSGDYRR +TPPCQANFCIFSRDGGSPCWPRWSRTPDLRWSACLGLPKCWDYRHEPPCPANLRWRLQWA +EIASLHSSLGDRARLSPTSASQVAGTTSMCHQTWLIFFFFFFETESRSITQAGVQWRDLS +SLQAPPPGYTPLSCLSLPSSWDYRHLPARPANFLHF* +>chr22_17 # 30943 # 32955 # -1 # ID=1_17;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.707 +MLLVFCLTRGRWLRLQNLGRPFPEAGGSHRTCAFGARECGAGCWGRGKEEAKWLPNISSK +EENTGLGPGKVPRTSRWQTKAALARPLSSRPQPAPRDHLARAFWQLRVSRAPTARRFARS +PSGDYLRALRACFLNDPARPRRGYEKFLQKKSRGEDPLKRPDWKVKCAKPGADGSPGGRR +GAGEAGRGRLPRGVGPGPGAAAARGPAPPPSRRGAPRRGGRGAGARWQLRPGAAAGSRPG +SLALNLLLSGSLERGSALRGRPRGLLSAAGGLGAGAPGSSGGGGCGCSTHLFSSDDILVT +RKDTWIPVLLLGGSRRRGRRRRCSGSSSPAQTLAFPEAPGAAAGTGRGGNMERAGHARAQ +GPGGERAGGRREGRRPPGSPPAAPPPGRPQQEEKGARRGEGGPRGPGGGEVLTAAPAAAL +GVGPRLAPHTRSHTRSLALPEQGRRKFCGCAWTPHTRRATVAVARGPRRGSPGATRTTDL +PNSQPSRPHNASSTAPARSPTLGPSPAPRAPPLPLTGLAPRMRSSRRPRTRRRRWPHRPS +PSPWVPSPCDGAAGPSRDFGSGSGSGSGGSQAVDPEIRDRDRGTAGEGGREPRTHAEAAR +APGAARREEQVCARRARAAGASLVLAEVFPRIAHTTGRKRNGVNFVLIQRQLQFPYYNVI +FLIQKRFIRM* +>chr22_18 # 33002 # 33439 # -1 # ID=1_18;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.482 +MGSHNPALLCLSSRYYFYYKSPNNTITKWMHPNQRNSLSINVLASFTSQRTLPLPTVQWE +YHLMKWVSTHAILQLRKTFTVLPRHTREPQKPSSSLALKRCLNLQAKPSNNRSVRRHFWS +SNKPVSSPTVRSVKGRRPYSQAPYS* +>chr22_19 # 35349 # 35690 # 1 # ID=1_19;partial=00;start_type=TTG;rbs_motif=TAAAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.377 +MILWSSSSSLSEAQVLTIGKPLSEYAHIKDLIIFVLMLKNFSEAFILFFPSLHRKFTLPS +WEAKETFYSTMFLTSSWKLMLEMGVGVGDGGGCTEAAGGRDRISEALSLAFFE* +>chr22_20 # 35821 # 35934 # -1 # ID=1_20;partial=00;start_type=ATG;rbs_motif=TATAA;rbs_spacer=14bp;genetic_code=4;gc_cont=0.342 +MVYIVMQYSFLSLISNSQIWKGEILLGEGRYKYRVAT* +>chr22_21 # 37683 # 38231 # 1 # ID=1_21;partial=00;start_type=ATG;rbs_motif=TTA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.499 +MISVFVFFFFRQSLTLLPRLECSGVILAHCSRRPPDSSDLPGSASQKAGITGACHHTQLI +FVFLVEMGVHHVGQAGLKLLTSGDLPASALPKCWDYRREPPCLAEIISFFIIAIACRYML +VVICKNVIERPGTVAHTGNPSTLGGWGGRITRSGVGDQPGQYGETPSLPKIQKLAGHSGG +HL* +>chr22_22 # 39452 # 40000 # -1 # ID=1_22;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.681 +RPREGAGDPGLHPLLAVTLRPHDLEGLGMRGSLNLRRERGSGDLQGWAVGGCSEKLGRPA +GRICQFAQSALGARAEGGRRCRVPRDAPERAGASWKRPKQCVWTGIPRKQWPGRSTPAGQ +RARLRDRRRGWASPRTPTRARWLPRVPKNLSPGVLGRLLIPEQGCTGLHFLDVCDKVAFS +LL* diff --git a/workflows/phageannotator/main.nf b/workflows/phageannotator/main.nf index c734838..13478c3 100644 --- a/workflows/phageannotator/main.nf +++ b/workflows/phageannotator/main.nf @@ -29,6 +29,7 @@ include { FASTA_VIRUS_CLASSIFICATION_GENOMAD } from '../../subworkflows/l include { FASTA_VIRUS_QUALITY_CHECKV } from '../../subworkflows/local/fasta_virus_quality_checkv/main' // TODO: Add to nf-core; Add nf-tests to nf-core modules include { FASTA_ALL_V_ALL_BLAST } from '../../subworkflows/local/fasta_all_v_all_blast/main' include { FASTA_PHAGE_HOST_IPHOP } from '../../subworkflows/local/fasta_phage_host_iphop/main' // TODO: Add to nf-core; Add nf-tests to nf-core modules +include { FASTA_PHAGE_FUNCTION_PHAROKKA } from '../../subworkflows/local/fasta_phage_function_pharokka/main' include { FASTA_MICRODIVERSITY_INSTRAIN } from '../../subworkflows/local/fasta_microdiversity_instrain/main' // TODO: Add to nf-core; Add nf-tests to nf-core modules @@ -44,7 +45,9 @@ include { FASTA_MICRODIVERSITY_INSTRAIN } from '../../subworkflows/l include { CAT_CAT as CAT_VIRUSES } from '../../modules/nf-core/cat/cat/main' include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main' include { GENOMAD_ENDTOEND as GENOMAD_TAXONOMY } from '../../modules/nf-core/genomad/endtoend/main' -include { GUNZIP } from '../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_CLUSTER_REPS } from '../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_VIRUS_PROTEINS } from '../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_VIRUS_GFF } from '../../modules/nf-core/gunzip/main' include { BACPHLIP } from '../../modules/nf-core/bacphlip/main' // @@ -294,6 +297,10 @@ workflow PHAGEANNOTATOR { /*---------------------------------------------------------------------------- Predict phage hosts ------------------------------------------------------------------------------*/ + // gunzip fasta for input into iphop, bacphlip, pharokka, + ch_anicluster_reps_fasta = GUNZIP_CLUSTER_REPS ( ch_anicluster_reps_fasta_gz ).gunzip + ch_versions = ch_versions.mix( GUNZIP_CLUSTER_REPS.out.versions ) + if ( !params.skip_iphop ){ // create channel from params.checkv_db if ( !params.iphop_db ){ @@ -305,7 +312,7 @@ workflow PHAGEANNOTATOR { // // SUBWORKFLOW: Download database and predict phage hosts // - ch_host_predictions_tsv = FASTA_PHAGE_HOST_IPHOP ( ch_anicluster_reps_fasta_gz, ch_iphop_db ).host_predictions_tsv + ch_host_predictions_tsv = FASTA_PHAGE_HOST_IPHOP ( ch_anicluster_reps_fasta, ch_iphop_db ).host_predictions_tsv ch_versions = ch_versions.mix( FASTA_PHAGE_HOST_IPHOP.out.versions ) } else { ch_host_predictions_tsv = Channel.empty() @@ -315,10 +322,6 @@ workflow PHAGEANNOTATOR { /*---------------------------------------------------------------------------- Predict virus lifestyle ------------------------------------------------------------------------------*/ - // gunzip fasta for input into bacphlip - ch_anicluster_reps_fasta = GUNZIP ( ch_anicluster_reps_fasta_gz ).gunzip - ch_versions = ch_versions.mix( GUNZIP.out.versions ) - if ( !params.skip_bacphlip ) { // // MODULE: Predict phage lifestyle using lysogeny specific genes @@ -331,7 +334,7 @@ workflow PHAGEANNOTATOR { /*---------------------------------------------------------------------------- - Identify protein-coding regions + Phage functional annotation ------------------------------------------------------------------------------*/ if ( !params.skip_prodigalgv ) { ch_prodigalgv_proteins_fna_gz = PRODIGAL_PRODIGALGV ( ch_anicluster_reps_fasta ).fna @@ -339,13 +342,39 @@ workflow PHAGEANNOTATOR { ch_versions = ch_versions.mix( PRODIGAL_PRODIGALGV.out.versions ) } else { ch_prodigalgv_proteins_faa_gz = Channel.empty() + ch_prodigalgv_proteins_gff_gz = Channel.empty() + } + + // gunzip fasta for input into iphop, bacphlip, pharokka, + ch_prodigalgv_proteins_faa = GUNZIP_VIRUS_GFF ( ch_prodigalgv_proteins_faa_gz ).gunzip + ch_versions = ch_versions.mix( GUNZIP_VIRUS_GFF.out.versions ) + + if ( !params.skip_pharokka ) { + // create channel from params.pharokka_db + if ( !params.pharokka_db ){ + ch_pharokka_db = null + } else { + ch_pharokka_db = Channel.value( file( params.pharokka_db, checkIfExists:true ) ) + } + + // + // SUBWORKFLOW: Functionally annotate phage sequences + // + ch_pharokka_ffn_gz = FASTA_PHAGE_FUNCTION_PHAROKKA ( ch_prodigalgv_proteins_faa, ch_pharokka_db ).pharokka_ffn_gz + ch_pharokka_output_tsv = FASTA_PHAGE_FUNCTION_PHAROKKA.out.pharokka_final_output_tsv + ch_versions = ch_versions.mix( FASTA_PHAGE_FUNCTION_PHAROKKA.out.versions ) + } else { ch_prodigalgv_proteins_fna_gz = Channel.empty() } /*---------------------------------------------------------------------------- - Analyze virus microdiversity + Analyze phage microdiversity ------------------------------------------------------------------------------*/ + // gunzip proteins for input into instrain + ch_prodigalgv_proteins_fna = GUNZIP_VIRUS_PROTEINS ( ch_prodigalgv_proteins_fna_gz ).gunzip + ch_versions = ch_versions.mix( GUNZIP_VIRUS_PROTEINS.out.versions ) + if ( !params.skip_instrain ) { // // MODULE: Generate instrain scaffold to bin file @@ -356,7 +385,7 @@ workflow PHAGEANNOTATOR { // // SUBWORKFLOW: Assess virus microdiversity within and across samples // - ch_gene_info_tsv = FASTA_MICRODIVERSITY_INSTRAIN ( ch_cluster_rep_alignment_bam, ch_anicluster_reps_fasta_gz, ch_prodigalgv_proteins_fna_gz, ch_stb_file_tsv ).gene_info_tsv + ch_gene_info_tsv = FASTA_MICRODIVERSITY_INSTRAIN ( ch_cluster_rep_alignment_bam, ch_anicluster_reps_fasta, ch_prodigalgv_proteins_fna, ch_stb_file_tsv ).gene_info_tsv ch_versions = ch_versions = ch_versions.mix(FASTA_MICRODIVERSITY_INSTRAIN.out.versions) } else { ch_gene_info_tsv = Channel.empty() @@ -373,7 +402,7 @@ workflow PHAGEANNOTATOR { host_predictions_tsv = ch_host_predictions_tsv marker_taxonomy_tsv = ch_marker_taxonomy_tsv // bacphlip_lifestyle_tsv = ch_bacphlip_lifestyle_tsv // Inconsistent hash - prodigalgv_proteins_faa_gz = ch_prodigalgv_proteins_faa_gz + pharokka_output_tsv = ch_pharokka_output_tsv instrain_gene_info = ch_gene_info_tsv versions = ch_versions } diff --git a/workflows/phageannotator/nextflow.config b/workflows/phageannotator/nextflow.config index 5ed75b3..f34f765 100644 --- a/workflows/phageannotator/nextflow.config +++ b/workflows/phageannotator/nextflow.config @@ -19,5 +19,6 @@ includeConfig '../../subworkflows/local/fasta_phage_host_iphop/nextflow.config' includeConfig '../../modules/nf-core/gunzip/nextflow.config' includeConfig '../../modules/nf-core/bacphlip/nextflow.config' includeConfig '../../modules/local/prodigal/prodigalgv/nextflow.config' +includeConfig '../../subworkflows/local/fasta_phage_function_pharokka/nextflow.config' includeConfig '../../modules/local/instrain/stb/nextflow.config' includeConfig '../../subworkflows/local/fasta_microdiversity_instrain/nextflow.config' diff --git a/workflows/phageannotator/tests/main.nf.test.snap b/workflows/phageannotator/tests/main.nf.test.snap index e4f6188..7368b45 100644 --- a/workflows/phageannotator/tests/main.nf.test.snap +++ b/workflows/phageannotator/tests/main.nf.test.snap @@ -73,67 +73,41 @@ ] ], "7": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,49a7f8cea341b7069a0943388d135e9f" - ] + ], "8": [ - [ - { - "id": "test2" - }, - "test2.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135" - ], - [ - { - "id": "test" - }, - "test.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135" - ] + ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", - "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", - "versions.yml:md5,6fd21ed738b35b25a1f47b313be8f47e", - "versions.yml:md5,755876cdfeb32585833c108ed6635839", - "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", - "versions.yml:md5,78b447897aac9e6a891f06a6c4af0e99", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", - "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", 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"versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ [ @@ -258,6 +206,6 @@ ] } ], - "timestamp": "2024-01-01T09:43:40.053838047" + "timestamp": "2024-01-23T16:08:46.939222078" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_instrain.nf.test.snap b/workflows/phageannotator/tests/skip_instrain.nf.test.snap index 15d80e2..23a1804 100644 --- a/workflows/phageannotator/tests/skip_instrain.nf.test.snap +++ b/workflows/phageannotator/tests/skip_instrain.nf.test.snap @@ -73,12 +73,7 @@ ] ], "7": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,49a7f8cea341b7069a0943388d135e9f" - ] + ], "8": [ @@ -86,38 +81,32 @@ "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + 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"versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ [ @@ -160,49 +149,38 @@ "all_samples_anicluster_representatives_taxonomy.tsv:md5,fb8440b1fd32f96414b71b76ec228df1" ] ], - "prodigalgv_proteins_faa_gz": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,49a7f8cea341b7069a0943388d135e9f" - ] + "pharokka_output_tsv": [ + ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", 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"2024-01-23T15:53:05.450284991" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_iphop.nf.test.snap b/workflows/phageannotator/tests/skip_iphop.nf.test.snap index 364b66c..a122b22 100644 --- a/workflows/phageannotator/tests/skip_iphop.nf.test.snap +++ b/workflows/phageannotator/tests/skip_iphop.nf.test.snap @@ -68,63 +68,38 @@ ] ], "7": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,49a7f8cea341b7069a0943388d135e9f" - ] + ], "8": [ - [ - { - "id": "test2" - }, - "test2.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135" - ], - [ - { - "id": "test" - }, - "test.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135" - ] + ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", - 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"versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", - "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ [ @@ -152,18 +127,7 @@ ], "instrain_gene_info": [ - [ 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"versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ [ @@ -252,6 +202,6 @@ ] } ], - "timestamp": "2024-01-01T10:27:28.605201593" + "timestamp": "2024-01-23T16:41:16.98960274" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_prodigalgv.nf.test b/workflows/phageannotator/tests/skip_pharokka.nf.test similarity index 93% rename from workflows/phageannotator/tests/skip_prodigalgv.nf.test rename to workflows/phageannotator/tests/skip_pharokka.nf.test index 2a3baa6..886277f 100644 --- a/workflows/phageannotator/tests/skip_prodigalgv.nf.test +++ b/workflows/phageannotator/tests/skip_pharokka.nf.test @@ -5,9 +5,9 @@ nextflow_workflow { workflow "PHAGEANNOTATOR" tag "workflows" tag "phageannotator" - tag "phageannotator_skip_prodigalgv" + tag "phageannotator_skip_pharokka" - test("Parameters: skip_prodigalgv = true") { + test("Parameters: skip_pharokka = true") { when { workflow { """ @@ -21,7 +21,7 @@ nextflow_workflow { } params { outdir = "$outputDir" - skip_prodigalgv = true + skip_pharokka = true mash_screen_min_score = 0.5 genomad_min_score = 0.01 genomad_max_fdr = 1 diff --git a/workflows/phageannotator/tests/skip_prodigalgv.nf.test.snap b/workflows/phageannotator/tests/skip_pharokka.nf.test.snap similarity index 100% rename from workflows/phageannotator/tests/skip_prodigalgv.nf.test.snap rename to workflows/phageannotator/tests/skip_pharokka.nf.test.snap diff --git a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap index a3515e2..41d4232 100644 --- a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap +++ b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap @@ -73,65 +73,39 @@ ] ], "7": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,ba02f7f691834c78746d404d5408b693" - ] + ], "8": [ - [ - { - "id": "test2" - }, - "test2.IS_gene_info.tsv:md5,0d05798c82a35fd4fd2787ff1cb9b607" - ], - [ - { - "id": "test" - }, - "test.IS_gene_info.tsv:md5,0d05798c82a35fd4fd2787ff1cb9b607" - ] + ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", 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"test.prodigalgv.faa.gz:md5,176c0114a2340a2b826d5c8bdd036a59" - ] + ], "8": [ ], "9": [ + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", - "versions.yml:md5,78b447897aac9e6a891f06a6c4af0e99", + "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", - "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ [ @@ -202,55 +186,39 @@ "test.filtered_taxonomy.tsv:md5,a62f9c3535da5e4d844e41da06ad1f99" ] ], - "prodigalgv_proteins_faa_gz": [ - [ - { - "id": "test2" - }, - "test2.prodigalgv.faa.gz:md5,e07d960760ce79284771082342475084" - ], - [ - { - "id": "test" - }, - "test.prodigalgv.faa.gz:md5,176c0114a2340a2b826d5c8bdd036a59" - ] + "pharokka_output_tsv": [ + ], "versions": [ + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", - "versions.yml:md5,78b447897aac9e6a891f06a6c4af0e99", + "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", - "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", + "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ [ @@ -286,6 +254,6 @@ ] } ], - "timestamp": "2024-01-01T09:49:58.902530636" + "timestamp": "2024-01-23T16:15:10.435647908" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/tags.yml b/workflows/phageannotator/tests/tags.yml index e62c387..f222b5d 100644 --- a/workflows/phageannotator/tests/tags.yml +++ b/workflows/phageannotator/tests/tags.yml @@ -14,7 +14,7 @@ phageannotator_skip_instrain: - workflows/phageannotator/** phageannotator_skip_iphop: - workflows/phageannotator/** -phageannotator_skip_prodigalgv: +phageannotator_skip_pharokka: - workflows/phageannotator/** phageannotator_skip_reference_containment: - workflows/phageannotator/** From c47298fd8e24408a573f4c1c22064b24b8ed95e5 Mon Sep 17 00:00:00 2001 From: Carson J Miller Date: Wed, 24 Jan 2024 21:27:23 +0000 Subject: [PATCH 02/23] Fixed nf-test test data issue --- conf/test_data.config | 2 +- nextflow.config | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/conf/test_data.config b/conf/test_data.config index 7726e35..aceb77a 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -29,7 +29,7 @@ params { blast_txt = "${params.phageannotator_test_data_base}/modules/local/anicluster/anicalc/blast.txt" ani_tsv = "${params.phageannotator_test_data_base}/modules/local/anicluster/aniclust/ani.tsv" clusters_tsv = "${params.phageannotator_test_data_base}/modules/local/anicluster/extractreps/clusters.tsv" - viromeqc = "${params.test_data_base}/modules/local/viromeqc/viromeqc/medians.csv" + viromeqc = "${params.phageannotator_test_data_base}/modules/local/viromeqc/viromeqc/medians.csv" } 'modules_nfcore' { checkv_test_db_tar = "${params.phageannotator_test_data_base}/modules/nfcore/checkv/endtoend/checkv_minimal_db.tar" diff --git a/nextflow.config b/nextflow.config index 30e1f9a..46650cd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -244,13 +244,12 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } - test { - includeConfig 'conf/test.config' - includeConfig 'conf/test_data.config' - } + test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } +includeConfig 'conf/test_data.config' + // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Singularity are enabled // Set to your registry if you have a mirror of containers From 0dbf933c1cc4baa0756e3d3cad528ebf5cd0ebdf Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Tue, 6 Feb 2024 10:05:59 -0800 Subject: [PATCH 03/23] Added pharokka and updated nf-tests --- .gitignore | 1 + main.nf | 2 +- modules.json | 4 +- .../anicluster/aniclust/tests/main.nf.test | 8 +- .../aniclust/tests/main.nf.test.snap | 8 +- .../anicluster/extractreps/tests/main.nf.test | 8 +- .../extractreps/tests/main.nf.test.snap | 8 +- modules/local/coverm/contig/nextflow.config | 7 +- .../local/coverm/contig/tests/main.nf.test | 8 +- .../coverm/contig/tests/main.nf.test.snap | 8 +- modules/local/prodigal/prodigalgv/main.nf | 2 - .../prodigalgv/tests/main.nf.test.snap | 14 +-- modules/local/viromeqc/viromeqc/main.nf | 4 +- .../viromeqc/viromeqc/tests/main.nf.test.snap | 32 ++++-- .../nf-core/checkv/downloaddatabase/main.nf | 2 + .../dumpsoftwareversions/environment.yml | 2 +- .../custom/dumpsoftwareversions/main.nf | 4 +- .../dumpsoftwareversions/nextflow.config | 9 -- .../dumpsoftwareversions/tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 50 +++++---- modules/nf-core/genomad/download/main.nf | 2 + modules/nf-core/instrain/profile/main.nf | 2 +- modules/nf-core/pharokka/pharokka/main.nf | 8 +- .../nf-core/pharokka/pharokka/nextflow.config | 2 +- .../samtools/sort/tests/main.nf.test.snap | 37 +++++++ nf-test.config | 2 +- .../fasta_microdiversity_instrain/main.nf | 12 ++- .../tests/main.nf.test | 4 +- .../tests/main.nf.test.snap | 30 +----- .../fasta_phage_function_pharokka/main.nf | 4 +- .../tests/main.nf.test.snap | 42 ++++++-- .../tests/nextflow.config | 2 +- .../tests/iphop_db_provided.nf.test | 2 +- .../tests/iphop_db_provided.nf.test.snap | 12 +-- .../fasta_phage_host_iphop/tests/main.nf.test | 2 +- .../tests/main.nf.test.snap | 4 +- .../tests/genomad_db_provided.nf.test.snap | 26 +---- .../tests/main.nf.test.snap | 4 +- .../tests/checkv_db_provided.nf.test.snap | 10 +- .../tests/main.nf.test.snap | 8 +- .../tests/main.nf.test | 2 +- .../tests/sketch_provided.nf.test | 6 +- .../tests/main.nf.test.snap | 16 ++- test.faa | 101 ------------------ tests/main.nf.test.snap | 98 ----------------- workflows/phageannotator/main.nf | 41 +++---- workflows/phageannotator/nextflow.config | 1 - workflows/phageannotator/tests/main.nf.test | 4 +- .../phageannotator/tests/main.nf.test.snap | 98 ++++++++++++++--- .../tests/skip_bacphlip.nf.test | 6 +- .../tests/skip_bacphlip.nf.test.snap | 100 ++++++++++++++--- .../phageannotator/tests/skip_checkv.nf.test | 4 +- .../tests/skip_checkv.nf.test.snap | 98 ++++++++++++++--- .../phageannotator/tests/skip_genomad.nf.test | 4 +- .../tests/skip_genomad.nf.test.snap | 98 ++++++++++++++--- .../tests/skip_genomad_taxonomy.nf.test | 4 +- .../tests/skip_genomad_taxonomy.nf.test.snap | 98 ++++++++++++++--- .../tests/skip_instrain.nf.test | 4 +- .../tests/skip_instrain.nf.test.snap | 66 ++++++++++-- .../phageannotator/tests/skip_iphop.nf.test | 4 +- .../tests/skip_iphop.nf.test.snap | 98 ++++++++++++++--- .../tests/skip_pharokka.nf.test | 4 +- .../tests/skip_pharokka.nf.test.snap | 44 +++++--- .../tests/skip_reference_containment.nf.test | 4 +- .../skip_reference_containment.nf.test.snap | 98 ++++++++++++++--- .../tests/skip_viromeqc.nf.test | 4 +- .../tests/skip_viromeqc.nf.test.snap | 70 ++++++++++-- .../tests/skip_virus_clustering.nf.test | 4 +- .../tests/skip_virus_clustering.nf.test.snap | 84 ++++++++++++--- 69 files changed, 1098 insertions(+), 568 deletions(-) delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/nextflow.config delete mode 100644 test.faa delete mode 100644 tests/main.nf.test.snap diff --git a/.gitignore b/.gitignore index f704e54..5ef6e6d 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ testing* *.pyc .nf-test* test.xml +nf-test-checklist.csv diff --git a/main.nf b/main.nf index 5c74754..6f0b292 100644 --- a/main.nf +++ b/main.nf @@ -28,7 +28,7 @@ Channel .fromSamplesheet("input") .multiMap { meta, fastq_1, fastq_2, fasta -> fastq_gz: [ meta, [ fastq_1, fastq_2 ] ] - fasta_gz: [ meta, [ fasta ] ] + fasta_gz: [ meta, fasta ] } .set { ch_input } diff --git a/modules.json b/modules.json index cbe3a35..ca0db53 100644 --- a/modules.json +++ b/modules.json @@ -48,7 +48,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "fastqc": { @@ -139,7 +139,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { diff --git a/modules/local/anicluster/aniclust/tests/main.nf.test b/modules/local/anicluster/aniclust/tests/main.nf.test index 4c43811..84e2407 100644 --- a/modules/local/anicluster/aniclust/tests/main.nf.test +++ b/modules/local/anicluster/aniclust/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "anicluster/aniclust" - test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv']") { + test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv']") { when { params { @@ -17,7 +17,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ], + input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ], [ file(params.test_data['modules_local']['ani_tsv'], checkIfExists: true ) ] ] """ } @@ -31,7 +31,7 @@ nextflow_process { } } - test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub") { + test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub") { options "-stub" @@ -41,7 +41,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ], + input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ], [ file(params.test_data['modules_local']['ani_tsv'], checkIfExists: true ) ] ] """ } diff --git a/modules/local/anicluster/aniclust/tests/main.nf.test.snap b/modules/local/anicluster/aniclust/tests/main.nf.test.snap index 87a4cf7..dbab532 100644 --- a/modules/local/anicluster/aniclust/tests/main.nf.test.snap +++ b/modules/local/anicluster/aniclust/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv']": { + "['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv']": { "content": [ { "0": [ @@ -26,9 +26,9 @@ ] } ], - "timestamp": "2024-01-17T22:30:47.969970392" + "timestamp": "2024-01-30T12:51:09.910625712" }, - "['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub": { + "['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv'] - stub": { "content": [ { "0": [ @@ -55,6 +55,6 @@ ] } ], - "timestamp": "2024-01-17T22:31:00.034885189" + "timestamp": "2024-01-30T12:51:20.189626093" } } \ No newline at end of file diff --git a/modules/local/anicluster/extractreps/tests/main.nf.test b/modules/local/anicluster/extractreps/tests/main.nf.test index 8a81428..8c46965 100644 --- a/modules/local/anicluster/extractreps/tests/main.nf.test +++ b/modules/local/anicluster/extractreps/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "anicluster/extractreps" - test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv']") { + test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv']") { when { params { @@ -17,7 +17,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ], + input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ], [ file(params.test_data['modules_local']['clusters_tsv'], checkIfExists: true ) ] ] """ } @@ -31,7 +31,7 @@ nextflow_process { } } - test("['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub") { + test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub") { options "-stub" @@ -41,7 +41,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists: true ) ], + input[0] = [ [ id: 'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true ) ], [ file(params.test_data['modules_local']['clusters_tsv'], checkIfExists: true ) ] ] """ } diff --git a/modules/local/anicluster/extractreps/tests/main.nf.test.snap b/modules/local/anicluster/extractreps/tests/main.nf.test.snap index 1ee5db9..17163e5 100644 --- a/modules/local/anicluster/extractreps/tests/main.nf.test.snap +++ b/modules/local/anicluster/extractreps/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv']": { + "['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv']": { "content": [ { "0": [ @@ -26,9 +26,9 @@ ] } ], - "timestamp": "2023-12-06T15:24:32.364815085" + "timestamp": "2024-01-30T12:16:45.282976267" }, - "['bacteroides_fragilis']['illumina']['contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub": { + "['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv'] - stub": { "content": [ { "0": [ @@ -55,6 +55,6 @@ ] } ], - "timestamp": "2024-01-17T22:49:59.94544688" + "timestamp": "2024-01-30T12:16:56.117800064" } } \ No newline at end of file diff --git a/modules/local/coverm/contig/nextflow.config b/modules/local/coverm/contig/nextflow.config index 52bc4c2..6a68acc 100644 --- a/modules/local/coverm/contig/nextflow.config +++ b/modules/local/coverm/contig/nextflow.config @@ -1,6 +1,11 @@ process { withName: COVERM_CONTIG { - ext.args = "--methods $params.coverm_metrics" + ext.args = [ + "--methods $params.coverm_metrics", + "--min-read-aligned-length $params.coverm_min_read_alignment", + "--min-read-percent-identity $params.coverm_min_percent_identity", + "--min-read-aligned-percent $params.coverm_min_percent_read_aligned", + ].join(' ').trim() publishDir = [ path: { "${params.outdir}/VirusAbundance/coverm/contig" }, mode: params.publish_dir_mode, diff --git a/modules/local/coverm/contig/tests/main.nf.test b/modules/local/coverm/contig/tests/main.nf.test index 297aa4c..eebf10a 100644 --- a/modules/local/coverm/contig/tests/main.nf.test +++ b/modules/local/coverm/contig/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "coverm/contig" - test("['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam']") { + test("['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam']") { when { params { @@ -16,7 +16,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_bam'], checkIfExists: true) ] ] + input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_paired_end_bam'], checkIfExists: true) ] ] """ } } @@ -29,7 +29,7 @@ nextflow_process { } } - test("['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam'] - stub") { + test("['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam'] - stub") { options "-stub" @@ -39,7 +39,7 @@ nextflow_process { } process { """ - input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_bam'], checkIfExists: true) ] ] + input[0] = [ [ id: 'all_samples' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_bam'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_paired_end_bam'], checkIfExists: true) ] ] """ } } diff --git a/modules/local/coverm/contig/tests/main.nf.test.snap b/modules/local/coverm/contig/tests/main.nf.test.snap index bf370c8..f8d3a63 100644 --- a/modules/local/coverm/contig/tests/main.nf.test.snap +++ b/modules/local/coverm/contig/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam']": { + "['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam']": { "content": [ { "0": [ @@ -26,9 +26,9 @@ ] } ], - "timestamp": "2023-11-13T11:52:17.129290553" + "timestamp": "2024-01-30T12:13:24.433507451" }, - "['bacteroides_fragilis']['test1_bam'] & ['bacteroides_fragilis']['test2_bam'] - stub": { + "['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam'] - stub": { "content": [ { "0": [ @@ -55,6 +55,6 @@ ] } ], - "timestamp": "2024-01-17T22:32:27.21624823" + "timestamp": "2024-01-30T12:13:34.750720485" } } \ No newline at end of file diff --git a/modules/local/prodigal/prodigalgv/main.nf b/modules/local/prodigal/prodigalgv/main.nf index 950b25d..fa04acf 100644 --- a/modules/local/prodigal/prodigalgv/main.nf +++ b/modules/local/prodigal/prodigalgv/main.nf @@ -46,8 +46,6 @@ process PRODIGAL_PRODIGALGV { touch ${prefix}.prodigalgv.faa gzip ${prefix}.prodigalgv.faa - gzip ${prefix}.prodigalgv.faa ${prefix}.prodigalgv.fna - cat <<-END_VERSIONS > versions.yml "${task.process}": prodigalgv: \$(echo \$(prodigal-gv --version 2>&1) | awk 'NF{ print \$NF }') diff --git a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap b/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap index 08c6aca..efaa6de 100644 --- a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap +++ b/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "all_samples" }, - "all_samples.prodigalgv.faa.gz:md5,6f28a3b4d319835fe5ce4864bc3b7c2c" + "all_samples.prodigalgv.faa.gz:md5,df108523d0141cb4cec62a09e2646348" ] ], "1": [ @@ -15,7 +15,7 @@ { "id": "all_samples" }, - "all_samples.prodigalgv.fna.gz:md5,d6eb37cf9a223db5dcf56538f5050c76" + "all_samples.prodigalgv.fna.gz:md5,c2a99be1dfbcea362f0e0ece02e7c0a6" ] ], "2": [ @@ -26,7 +26,7 @@ { "id": "all_samples" }, - "all_samples.prodigalgv.faa.gz:md5,6f28a3b4d319835fe5ce4864bc3b7c2c" + "all_samples.prodigalgv.faa.gz:md5,df108523d0141cb4cec62a09e2646348" ] ], "fna": [ @@ -34,7 +34,7 @@ { "id": "all_samples" }, - "all_samples.prodigalgv.fna.gz:md5,d6eb37cf9a223db5dcf56538f5050c76" + "all_samples.prodigalgv.fna.gz:md5,c2a99be1dfbcea362f0e0ece02e7c0a6" ] ], "versions": [ @@ -42,7 +42,7 @@ ] } ], - "timestamp": "2023-12-06T15:25:14.501666251" + "timestamp": "2024-01-24T13:41:31.810729686" }, "['sarscov2']['genome']['genome_fasta'] - stub": { "content": [ @@ -87,6 +87,6 @@ ] } ], - "timestamp": "2024-01-17T22:52:02.155249524" + "timestamp": "2024-01-24T13:41:41.320396288" } -} +} \ No newline at end of file diff --git a/modules/local/viromeqc/viromeqc/main.nf b/modules/local/viromeqc/viromeqc/main.nf index d222b15..5857c13 100644 --- a/modules/local/viromeqc/viromeqc/main.nf +++ b/modules/local/viromeqc/viromeqc/main.nf @@ -12,8 +12,8 @@ process VIROMEQC_VIROMEQC { path(viromeqc_index) output: - path("${prefix}.viromeqc.tsv") , emit: enrichment - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.viromeqc.tsv") , emit: enrichment + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/viromeqc/viromeqc/tests/main.nf.test.snap b/modules/local/viromeqc/viromeqc/tests/main.nf.test.snap index 68efa59..d76868a 100644 --- a/modules/local/viromeqc/viromeqc/tests/main.nf.test.snap +++ b/modules/local/viromeqc/viromeqc/tests/main.nf.test.snap @@ -3,38 +3,58 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "1": [ "versions.yml:md5,2877c7f2bffbd5cd7c2cccc730b9f093" ], "enrichment": [ - "test.viromeqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "versions": [ "versions.yml:md5,2877c7f2bffbd5cd7c2cccc730b9f093" ] } ], - "timestamp": "2024-01-17T22:42:18.098035496" + "timestamp": "2024-01-30T12:59:31.945315" }, "sarscov2 - illumina - test_1_fastq_gz": { "content": [ { "0": [ - "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + ] ], "1": [ "versions.yml:md5,1d793f1196d60e1c94969fb0a103e353" ], "enrichment": [ - "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + ] ], "versions": [ "versions.yml:md5,1d793f1196d60e1c94969fb0a103e353" ] } ], - "timestamp": "2023-12-28T13:22:47.999767324" + "timestamp": "2024-01-30T12:59:11.908627959" } } \ No newline at end of file diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index bc5086f..2043d55 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,6 +18,8 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index f0c63f6..9b3272b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 7685b33..f218761 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config deleted file mode 100644 index 055400d..0000000 --- a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index eec1db1..b1e1630 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -31,7 +31,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } ) } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 4274ed5..5f59a93 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -1,27 +1,33 @@ { "Should run without failures": { "content": [ - { - "0": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ], - "1": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "2": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "versions": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "yml": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ] - } + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-09T23:01:18.710682" } -} +} \ No newline at end of file diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index a2ac6ec..632d494 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,6 +16,8 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy genomad \\ download-database . diff --git a/modules/nf-core/instrain/profile/main.nf b/modules/nf-core/instrain/profile/main.nf index a46fbdb..d30026a 100644 --- a/modules/nf-core/instrain/profile/main.nf +++ b/modules/nf-core/instrain/profile/main.nf @@ -16,7 +16,7 @@ process INSTRAIN_PROFILE { output: tuple val(meta), path("*.IS") , emit: profile tuple val(meta), path("*.IS/output/*.IS_SNVs.tsv") , emit: snvs - tuple val(meta), path("*.IS/output/*.IS_gene_info.tsv") , emit: gene_info + tuple val(meta), path("*.IS/output/*.IS_gene_info.tsv") , emit: gene_info , optional: true tuple val(meta), path("*.IS/output/*.IS_genome_info.tsv") , emit: genome_info tuple val(meta), path("*.IS/output/*.IS_linkage.tsv") , emit: linkage tuple val(meta), path("*.IS/output/*.IS_mapping_info.tsv") , emit: mapping_info diff --git a/modules/nf-core/pharokka/pharokka/main.nf b/modules/nf-core/pharokka/pharokka/main.nf index 677e331..3379684 100644 --- a/modules/nf-core/pharokka/pharokka/main.nf +++ b/modules/nf-core/pharokka/pharokka/main.nf @@ -15,7 +15,7 @@ process PHAROKKA_PHAROKKA { tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv") , emit: cds_final_merged_output tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_functions.tsv") , emit: cds_functions tuple val(meta), path("${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv") , emit: length_gc_cds_density - tuple val(meta), path("${prefix}_pharokka/p*.ffn.gz") , emit: ffn + tuple val(meta), path("${prefix}_pharokka/${prefix}.gbk.gz") , emit: gbk tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_card.tsv") , emit: card , optional: true tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv") , emit: vfdb , optional: true tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv") , emit: mash , optional: true @@ -38,7 +38,7 @@ process PHAROKKA_PHAROKKA { --prefix ${prefix} \\ $args - gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff + gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff ${prefix}_pharokka/*.gbk cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -52,6 +52,8 @@ process PHAROKKA_PHAROKKA { """ mkdir -p ${prefix}_pharokka + touch ${prefix}_pharokka/prodigal-gv.ffn + touch ${prefix}_pharokka/prodigal-gv.faa touch ${prefix}_pharokka/${prefix}.gbk touch ${prefix}_pharokka/${prefix}.log touch ${prefix}_pharokka/${prefix}_cds_functions.tsv @@ -60,6 +62,8 @@ process PHAROKKA_PHAROKKA { touch ${prefix}_pharokka/${prefix}_top_hits_inphared touch ${prefix}_pharokka/${prefix} + gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff ${prefix}_pharokka/*.gbk + cat <<-END_VERSIONS > versions.yml "${task.process}": pharokka: \$(pharokka.py --version) diff --git a/modules/nf-core/pharokka/pharokka/nextflow.config b/modules/nf-core/pharokka/pharokka/nextflow.config index 34f3bbe..41d4da6 100644 --- a/modules/nf-core/pharokka/pharokka/nextflow.config +++ b/modules/nf-core/pharokka/pharokka/nextflow.config @@ -1,7 +1,7 @@ process { withName: PHAROKKA_PHAROKKA { ext.args = [ - "--genbank --meta", + "--meta", ].join(' ').trim() publishDir = [ path: { "${params.outdir}/PhageFunction/pharokka/pharokka" }, diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index a43566d..07fc610 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -35,5 +35,42 @@ } ], "timestamp": "2023-10-17T17:21:46.5427968" + }, + "test_samtools_sort_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + ] + } + ], + "timestamp": "2024-01-30T15:07:33.996526252" } } \ No newline at end of file diff --git a/nf-test.config b/nf-test.config index cb656b9..d97921a 100644 --- a/nf-test.config +++ b/nf-test.config @@ -3,7 +3,7 @@ config { testsDir "." // nf-test directory including temporary files for each test - workDir "/tmp" + workDir ".nf-tests/" // location of library folder that is added automatically to the classpath libDir "lib/" diff --git a/subworkflows/local/fasta_microdiversity_instrain/main.nf b/subworkflows/local/fasta_microdiversity_instrain/main.nf index 7516b99..f2634b9 100644 --- a/subworkflows/local/fasta_microdiversity_instrain/main.nf +++ b/subworkflows/local/fasta_microdiversity_instrain/main.nf @@ -17,9 +17,17 @@ workflow FASTA_MICRODIVERSITY_INSTRAIN { ch_versions = Channel.empty() // remove meta information for instrain profile inputs - ch_stb_file_tsv_nometa = instrain_stb.map { it[1] }.first() ch_genome_fasta_nometa = genome_fasta.map { it[1] }.first() - ch_proteins_fna_nometa = proteins_fna.map { it[1] }.first() + if ( proteins_fna ){ + ch_proteins_fna_nometa = proteins_fna.map { it[1] }.first() + } else { + ch_proteins_fna_nometa = [] + } + if ( instrain_stb ){ + ch_stb_file_tsv_nometa = instrain_stb.map { it[1] }.first() + } else { + ch_stb_file_tsv_nometa = [] + } // // MODULE: Profile microdiveristy within each sample diff --git a/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test b/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test index 1f3a854..1f108be 100644 --- a/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test +++ b/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test @@ -23,8 +23,8 @@ nextflow_workflow { [ [ id:'test' ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], [ [ id:'test2' ], file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) ] ) - input[1] = Channel.of([ [ id: 'reference_fasta' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_gz'], checkIfExists: true) ]) - input[2] = Channel.of([ [ id: 'proteins_fasta' ], file(params.test_data['modules_nfcore']['proteins_fna_gz'], checkIfExists: true) ]) + input[1] = Channel.of([ [ id: 'reference_fasta' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]) + input[2] = null input[3] = Channel.of([ [ id: 'instrain_stb' ], file(params.test_data['modules_nfcore']['instrain_stb'], checkIfExists: true) ]) """ } diff --git a/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test.snap b/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test.snap index fe19450..0b88ac5 100644 --- a/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_microdiversity_instrain/tests/main.nf.test.snap @@ -3,47 +3,23 @@ "content": [ { "0": [ - [ - { - "id": "test2" - }, - "test2.IS_gene_info.tsv:md5,43f12c345cca84b8a852fd056cc325ad" - ], - [ - { - "id": "test" - }, - "test.IS_gene_info.tsv:md5,af8e354716ea235b3487862abd837884" - ] + ], "1": [ - "versions.yml:md5,6b5a937ad6a7261cd10742b95cb28df2", "versions.yml:md5,816a6bc0dc4c7fe8dee2a3cd012b38e2", "versions.yml:md5,ca6a3c4a779d53a24bd7303d2f0736da", "versions.yml:md5,ca6a3c4a779d53a24bd7303d2f0736da" ], "gene_info_tsv": [ - [ - { - "id": "test2" - }, - "test2.IS_gene_info.tsv:md5,43f12c345cca84b8a852fd056cc325ad" - ], - [ - { - "id": "test" - }, - "test.IS_gene_info.tsv:md5,af8e354716ea235b3487862abd837884" - ] + ], "versions": [ - "versions.yml:md5,6b5a937ad6a7261cd10742b95cb28df2", "versions.yml:md5,816a6bc0dc4c7fe8dee2a3cd012b38e2", "versions.yml:md5,ca6a3c4a779d53a24bd7303d2f0736da", "versions.yml:md5,ca6a3c4a779d53a24bd7303d2f0736da" ] } ], - "timestamp": "2023-12-06T15:49:43.895338311" + "timestamp": "2024-01-31T08:59:05.93091557" } } \ No newline at end of file diff --git a/subworkflows/local/fasta_phage_function_pharokka/main.nf b/subworkflows/local/fasta_phage_function_pharokka/main.nf index d25dec8..d119fea 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/main.nf +++ b/subworkflows/local/fasta_phage_function_pharokka/main.nf @@ -27,12 +27,12 @@ workflow FASTA_PHAGE_FUNCTION_PHAROKKA { // // MODULE: Functionally annotate phages // - ch_pharokka_ffn_gz = PHAROKKA_PHAROKKA ( virus_fasta, ch_pharokka_db ).ffn + ch_pharokka_gbk_gz = PHAROKKA_PHAROKKA ( virus_fasta, ch_pharokka_db ).gbk pharokka_final_output_tsv = PHAROKKA_PHAROKKA.out.cds_final_merged_output ch_versions = ch_versions.mix(PHAROKKA_PHAROKKA.out.versions.first()) emit: versions = ch_versions // [ versions.yml ] - pharokka_ffn_gz = ch_pharokka_ffn_gz // [ [ meta ], ffn.gz ] + pharokka_gbk_gz = ch_pharokka_gbk_gz // [ [ meta ], gbk.gz ] pharokka_final_output_tsv = pharokka_final_output_tsv // [ [ meta ], tsv ] } diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap index 83b6c12..cc2128c 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -3,25 +3,47 @@ "content": [ { "0": [ - "versions.yml:md5,7715e330cd5621f95141e256b567ec19" + "versions.yml:md5,7715e330cd5621f95141e256b567ec19", + "versions.yml:md5,b225eb2829469045a5bda2c5d7a69009" ], "1": [ - + [ + { + "id": "test" + }, + "test.gbk.gz:md5,e719cd124ccca0524df508cd178e853e" + ] ], "2": [ - - ], - "pharokka_ffn_gz": [ - + [ + { + "id": "test" + }, + "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" + ] ], "pharokka_final_output_tsv": [ - + [ + { + "id": "test" + }, + "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" + ] + ], + "pharokka_gbk_gz": [ + [ + { + "id": "test" + }, + "test.gbk.gz:md5,e719cd124ccca0524df508cd178e853e" + ] ], "versions": [ - "versions.yml:md5,7715e330cd5621f95141e256b567ec19" + "versions.yml:md5,7715e330cd5621f95141e256b567ec19", + "versions.yml:md5,b225eb2829469045a5bda2c5d7a69009" ] } ], - "timestamp": "2024-01-24T09:28:21.667432563" + "timestamp": "2024-01-24T14:00:39.927815714" } -} \ No newline at end of file +} diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config b/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config index 4fdbc96..a3c1166 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: PHAROKKA_PHAROKKA { - ext.args = "--locustag TEST --meta" + ext.args = "--locustag TEST" } } diff --git a/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test b/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test index 1e1a2f3..d7f2dfd 100644 --- a/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test +++ b/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ [ id:'test' ], [ file('https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true) ] ]) + input[0] = Channel.of([ [ id:'test' ], [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]) input[1] = Channel.of([ file(params.iphop_db, checkIfExists:true ) ]) """ } diff --git a/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test.snap b/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test.snap index 452f2bc..a3bacfc 100644 --- a/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test.snap +++ b/subworkflows/local/fasta_phage_host_iphop/tests/iphop_db_provided.nf.test.snap @@ -7,27 +7,25 @@ { "id": "test" }, - "Host_prediction_to_genus_m90.csv:md5,e529062e32656f9e9e1737ebd66c4e83" + "Host_prediction_to_genus_m90.csv:md5,6f80d41b3a5ef039141effe4b644bb65" ] ], "1": [ - "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80", - "versions.yml:md5,9a3afe922371942954848605293c0700" + "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80" ], "host_predictions_tsv": [ [ { "id": "test" }, - "Host_prediction_to_genus_m90.csv:md5,e529062e32656f9e9e1737ebd66c4e83" + "Host_prediction_to_genus_m90.csv:md5,6f80d41b3a5ef039141effe4b644bb65" ] ], "versions": [ - "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80", - "versions.yml:md5,9a3afe922371942954848605293c0700" + "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80" ] } ], - "timestamp": "2023-11-16T16:15:22.426800093" + "timestamp": "2024-01-31T10:23:05.542262514" } } \ No newline at end of file diff --git a/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test b/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test index 1523a93..29d6d95 100644 --- a/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test +++ b/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_workflow { } workflow { """ - input[0] = Channel.of([ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ] ]) + input[0] = Channel.of([ [ id:'test' ], [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ]) input[1] = null """ } diff --git a/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test.snap index 44cebb6..1fe97fe 100644 --- a/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_host_iphop/tests/main.nf.test.snap @@ -13,7 +13,6 @@ "1": [ "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80", "versions.yml:md5,6d962b190899f9580909b28917ffa748", - "versions.yml:md5,9a3afe922371942954848605293c0700", "versions.yml:md5,c8e1743aa09ef3013ef7ddb1edc8c43e" ], "host_predictions_tsv": [ @@ -27,11 +26,10 @@ "versions": [ "versions.yml:md5,41c2135a3578a7a52a23fd3243c22e80", "versions.yml:md5,6d962b190899f9580909b28917ffa748", - "versions.yml:md5,9a3afe922371942954848605293c0700", "versions.yml:md5,c8e1743aa09ef3013ef7ddb1edc8c43e" ] } ], - "timestamp": "2023-12-11T10:11:40.484898808" + "timestamp": "2024-01-31T10:24:30.812222892" } } \ No newline at end of file diff --git a/subworkflows/local/fasta_virus_classification_genomad/tests/genomad_db_provided.nf.test.snap b/subworkflows/local/fasta_virus_classification_genomad/tests/genomad_db_provided.nf.test.snap index 01dccc3..bfaf26c 100644 --- a/subworkflows/local/fasta_virus_classification_genomad/tests/genomad_db_provided.nf.test.snap +++ b/subworkflows/local/fasta_virus_classification_genomad/tests/genomad_db_provided.nf.test.snap @@ -44,12 +44,6 @@ ] ], "1": [ - [ - { - "id": "test2" - }, - "genome_virus.fna.gz:md5,1b10bd0f19c8c41c426c0a75ea38efb9" - ], [ { "id": "test" @@ -58,12 +52,6 @@ ] ], "2": [ - [ - { - "id": "test2" - }, - "genome_virus_summary.tsv:md5,6899de91e735b5b930347d9d0fda8a7a" - ], [ { "id": "test" @@ -119,12 +107,6 @@ "versions.yml:md5,6b3b022e67e97057826d98ef627a82fb" ], "virus_summaries_tsv": [ - [ - { - "id": "test2" - }, - "genome_virus_summary.tsv:md5,6899de91e735b5b930347d9d0fda8a7a" - ], [ { "id": "test" @@ -133,12 +115,6 @@ ] ], "viruses_fna_gz": [ - [ - { - "id": "test2" - }, - "genome_virus.fna.gz:md5,1b10bd0f19c8c41c426c0a75ea38efb9" - ], [ { "id": "test" @@ -148,6 +124,6 @@ ] } ], - "timestamp": "2023-12-06T15:47:41.364409205" + "timestamp": "2024-01-31T11:00:51.118691047" } } \ No newline at end of file diff --git a/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test.snap b/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test.snap index b38cbc1..d5148b2 100644 --- a/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test.snap @@ -152,6 +152,6 @@ ] } ], - "timestamp": "2024-01-05T12:53:16.390470203" + "timestamp": "2024-01-31T10:56:21.03653297" } -} +} \ No newline at end of file diff --git a/subworkflows/local/fasta_virus_quality_checkv/tests/checkv_db_provided.nf.test.snap b/subworkflows/local/fasta_virus_quality_checkv/tests/checkv_db_provided.nf.test.snap index c84f3e4..251c90d 100644 --- a/subworkflows/local/fasta_virus_quality_checkv/tests/checkv_db_provided.nf.test.snap +++ b/subworkflows/local/fasta_virus_quality_checkv/tests/checkv_db_provided.nf.test.snap @@ -45,8 +45,7 @@ ] ], "3": [ - "versions.yml:md5,bde8142f045061369c16cd56d51698ed", - "versions.yml:md5,e4d4311cae4bcb6711e82eef25b187ff" + "versions.yml:md5,bde8142f045061369c16cd56d51698ed" ], "proviruses_fna_gz": [ [ @@ -77,8 +76,7 @@ ] ], "versions": [ - "versions.yml:md5,bde8142f045061369c16cd56d51698ed", - "versions.yml:md5,e4d4311cae4bcb6711e82eef25b187ff" + "versions.yml:md5,bde8142f045061369c16cd56d51698ed" ], "viruses_fna_gz": [ [ @@ -96,6 +94,6 @@ ] } ], - "timestamp": "2024-01-08T08:57:05.04137914" + "timestamp": "2024-01-31T11:25:22.342656511" } -} +} \ No newline at end of file diff --git a/subworkflows/local/fasta_virus_quality_checkv/tests/main.nf.test.snap b/subworkflows/local/fasta_virus_quality_checkv/tests/main.nf.test.snap index 6755e94..99b5622 100644 --- a/subworkflows/local/fasta_virus_quality_checkv/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_virus_quality_checkv/tests/main.nf.test.snap @@ -46,8 +46,7 @@ ], "3": [ "versions.yml:md5,58c018640348d4755b08dd850a477465", - "versions.yml:md5,bde8142f045061369c16cd56d51698ed", - "versions.yml:md5,e4d4311cae4bcb6711e82eef25b187ff" + "versions.yml:md5,bde8142f045061369c16cd56d51698ed" ], "proviruses_fna_gz": [ [ @@ -79,8 +78,7 @@ ], "versions": [ "versions.yml:md5,58c018640348d4755b08dd850a477465", - "versions.yml:md5,bde8142f045061369c16cd56d51698ed", - "versions.yml:md5,e4d4311cae4bcb6711e82eef25b187ff" + "versions.yml:md5,bde8142f045061369c16cd56d51698ed" ], "viruses_fna_gz": [ [ @@ -98,6 +96,6 @@ ] } ], - "timestamp": "2023-12-06T15:52:54.392852716" + "timestamp": "2024-01-31T11:24:04.386626815" } } \ No newline at end of file diff --git a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test index 1551124..454d82f 100644 --- a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test +++ b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_workflow { [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test2_1_fastq_gz'], checkIfExists:true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] ] ) input[1] = Channel.of([ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists:true) ] ]) - input[2] = Channel.of([ [ id:'reference_viruses' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[2] = Channel.of([ [ id:'reference_viruses' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) input[3] = null """ } diff --git a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test index c7c78b1..9c14724 100644 --- a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test +++ b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test @@ -14,8 +14,8 @@ nextflow_workflow { when { params { outdir = "$outputDir" - reference_virus_fasta = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz' - reference_virus_sketch = 'https://github.com/nf-core/test-datasets/raw/phageannotator/modules/local/mash/paste/bacteroides_fragilis_contigs1.msh' + reference_virus_fasta = "$params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz']" + reference_virus_sketch = "$params.test_data['modules_local']['mash_sketch1_msh']" } workflow { """ @@ -24,7 +24,7 @@ nextflow_workflow { [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test2_1_fastq_gz'], checkIfExists:true), file(params.test_data['bacteroides_fragilis']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] ] ) input[1] = Channel.of([ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists:true) ] ]) - input[2] = Channel.of([ [ id:'reference_viruses' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[2] = Channel.of([ [ id:'reference_viruses' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) input[3] = Channel.of([ [ id:'reference_viruses' ], [ file(params.test_data['modules_local']['mash_sketch1_msh'], checkIfExists:true) ] ]) """ } diff --git a/subworkflows/local/fastq_virus_enrichment_viromeqc/tests/main.nf.test.snap b/subworkflows/local/fastq_virus_enrichment_viromeqc/tests/main.nf.test.snap index 538a5c0..9eb2dc9 100644 --- a/subworkflows/local/fastq_virus_enrichment_viromeqc/tests/main.nf.test.snap +++ b/subworkflows/local/fastq_virus_enrichment_viromeqc/tests/main.nf.test.snap @@ -3,14 +3,24 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + ] ], "1": [ "versions.yml:md5,c26288b67351c3bdaad635c87a0249e7", "versions.yml:md5,f771871e8cbe81944f6d5fbbc56cc7a5" ], "enrichment_tsv": [ - "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,6acbffc97f75774cf9fcc953b98913ed" + ] ], "versions": [ "versions.yml:md5,c26288b67351c3bdaad635c87a0249e7", @@ -18,6 +28,6 @@ ] } ], - "timestamp": "2023-12-28T13:57:38.935414881" + "timestamp": "2024-01-31T13:33:23.516887168" } } \ No newline at end of file diff --git a/test.faa b/test.faa deleted file mode 100644 index 4053a09..0000000 --- a/test.faa +++ /dev/null @@ -1,101 +0,0 @@ ->chr22_1 # 4575 # 4697 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.398 -MEKLINLTDIVKQEKKDETQKLCDSSLCLRLFSLQWGRVV* ->chr22_2 # 5954 # 6520 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=TTA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.337 -MSKTSLKYFSLKITCGVNRLWCFYYLKTTFILQMFLRRGECEGRGQNREEFEWITFFISI -LLIWGMSLREGWKLWEYIVYRKRINSSSWMGLWRLNCKSQHWQHPQLIILGDRIIQLGCF -ININNTIFNYYIKNFKYIYVPWPGKPVFYFHKNYFYCMKRLWGLAQNICGPDKIGLVTLP -QKENGKKK* ->chr22_3 # 8336 # 8563 # -1 # ID=1_3;partial=00;start_type=ATG;rbs_motif=TTAA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.298 -MVKEKPTLTFCNVYENWKQNQFACSLTSFLGSDLQMTWKKVHLPIAYTYIHMYVYIHIFL -KIQAYNSLCLKEVNI* ->chr22_4 # 11642 # 11989 # -1 # ID=1_4;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.405 -MLHFIVFKHQFQSDDFCFLFWMQWFLRFQTVCRPLAQYLKYLMDMVINLKLFWKKSPADR -APFSTGSVSQEPKSRWGSLSVSLEQKPQRAFLQGNILLQEIKTETTEALLGVESS* ->chr22_5 # 12499 # 12948 # -1 # ID=1_5;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.464 -MAHACNPSTLGGQGGWITWGQELETSLANTLSLLKIQKLAGHGSWAPVIPANCVHKLITA -PKCRTKFSSKWRTFFFFSNWSIRREESTCTAIHTDIMDDWLDCAFTCGVHCRGHGKYSCL -RVFVNLTHSAQKALLHYNEEAVQINPKVL* ->chr22_6 # 13971 # 14360 # -1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=TTAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.454 -MSSASCVHRPQNPSIPESPFPTVAAPLLAGTPSSGLVFPLQKRTRSANLRLPYADAKYYV -SYFIPSQSFWLQTSFYFNFITIGFFLMLLLLFVCFFWDRVFLCHLGWSKVAQSQLTATSA -SRVQAILLP* ->chr22_7 # 14374 # 14874 # -1 # ID=1_7;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.477 -MQHMFEKQFYTVDRVEKMALWKFSSNSQNAPAGKVDPGKFRGHMPLYSEKYFLSFFFFFR -WSLPLSPRLECTGAISAHCKLRLPGSRHSPASAARVTGITGLRHHAWLTFCIFSRDGRGF -TVLARMVSISWPHDPPASASQSTGITDVSHCARLKNIFISSSTFIS* ->chr22_8 # 16449 # 16853 # -1 # ID=1_8;partial=00;start_type=ATG;rbs_motif=AATAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.420 -MVVNTCSPSYWGAEVEGFLEPRKSRLQWAVIGPLHSSLGDKVRPFLKKKKKKDFNLQKHW -SSDEEKKVSIPNCEKNCEETIENKTTEKSCHSLPVLSLHGPASSHVYWVVSPESLFIYLF -IFEMESCSVTQAGV* ->chr22_9 # 17198 # 17380 # 1 # ID=1_9;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.492 -MTGLRIAQMDEQFPRLIPSLHYPSQPLISFISQDLVLIFLPCFLRIVAIVPWLLDQPGAQ -* ->chr22_10 # 18024 # 18590 # -1 # ID=1_10;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.519 -MAWSWLTASTSRVQVILLPQPPSSWDYRGPPLSQTNFIYLFIYFLRWHLTLSPSLECSGV -ISAHCNLHLPGSRDSSVSASWVAGTTGVRHHARIIFVFLVETGSHHNGQAGLELLTSWST -HLSLPKCWDYRHEPLPPANFFEFFVETGFHHVGQAGLEPLTSNDSPASTSQSAGITGMNH -RPQHKCPL* ->chr22_11 # 20113 # 20742 # -1 # ID=1_11;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.459 -MRLVPFQFSTFFVFFFWETESCSVAQAGVQWRDLGSLQPPPPRFKRFSCLSLLNSWDYRC -APPRPAIFCIFSRDGVSPYWPGWSRTPDLMILPPQPPKVLGLQARATVPSQFLTFSFCVS -IRCSSFPMIRAGFNSIKIFKLSTYVGFGRAKHSAAISSQLFEHSLHDILTYMDLCLDVTL -GVWKHQLQLTRVVSPSCCGYLKKKKGLSS* ->chr22_12 # 20878 # 22551 # -1 # ID=1_12;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.568 -MDSTVPSALELPQRLALNPRESPRSPEEEEPHLLSSLAAVQTLASVIRPCYGPHGRQKFL -VTMKGETVCTGCATAILRALELEHPAAWLLREAGQTQAENSGDGTAFVVLLTEALLEQAE -QLLKAGLPRPQLREAYATATAEVLATLPSLAIQSLGPLEDPSWALHSVMNTHTLSPMDHL -TKLVAHACWAIKELDGSFKPERVGVCALPGGTLEDSCLLPGLAISGKLCGQMATVLSGAR -VALFACPFGPAHPNAPATARLSSPADLAQFSKGSDQLLEKQVGQLAAAGINVAVVLGEVD -EETLTLADKYGIVVIQARSWMEIIYLSEVLDTPLLPRLLPPQRPGKCQRVYRQELGDGLA -VVFEWECTGTPALTVVLRGATTQGLRSAEQAVYHGIDAYFQLCQDPRLIPGAGATEMALA -KMLSDKGSRLEGPSGPAFLAFAWALKYLPKTLAENAGLAVSDVMAEMSGVHQGGNLLMGV -GTEGIINVAQEGVWDTLIVKAQGFRAVAEVVLQLVTVDEIVVAKKSPTHQEIWNPDSKKT -KKHPPPVETKKILGLNN* ->chr22_13 # 23191 # 23703 # 1 # ID=1_13;partial=00;start_type=GTG;rbs_motif=TTTTA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.489 -MFLSVVQAGLEFLASREPSTLASQSARTTGVSHHLTHPFFFFFFETESHSVAQAGVQWYN -LSSLQPPPPRFKQFSCLSLSVAGITGASHHARLIFYIFSRDRGISPCWPWLARLVSNSWP -QVIRPPRPPKVLGLQVWATAPGLFFLFEKELRDDVCVLFCFGVTFSCSTV* ->chr22_14 # 25201 # 25689 # 1 # ID=1_14;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.474 -MLNQCTICKVAHSLSFSAISCGFFKLLSQGTRKLCCFQSALSFYGEVFAITSDDTIWLGH -CAHFLQSYFLLAPSCIHQSLRCPPGAIFLPAAELWPWWVQGGWCAEQGLRRRGSVLSRNV -SKEILFGLRTMNDYFEHFWFWRLHLDQAWSSKFRLLKACTSE* ->chr22_15 # 25895 # 26122 # -1 # ID=1_15;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.443 -MPELHLAQASQSAGIIGSSHGHWPVVFILFIYLFIYLFIYFLRLSLALLPRLEYSGAILA -HCNLSTSQVQEILVP* ->chr22_16 # 27925 # 28575 # 1 # ID=1_16;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.524 -MIYFTEITYIAIWIFFLRRSFALVAQARVQWRDLGSLQPPPPGFKQFSCLSLQNSGDYRR -TPPCQANFCIFSRDGGSPCWPRWSRTPDLRWSACLGLPKCWDYRHEPPCPANLRWRLQWA -EIASLHSSLGDRARLSPTSASQVAGTTSMCHQTWLIFFFFFFETESRSITQAGVQWRDLS -SLQAPPPGYTPLSCLSLPSSWDYRHLPARPANFLHF* ->chr22_17 # 30943 # 32955 # -1 # ID=1_17;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.707 -MLLVFCLTRGRWLRLQNLGRPFPEAGGSHRTCAFGARECGAGCWGRGKEEAKWLPNISSK -EENTGLGPGKVPRTSRWQTKAALARPLSSRPQPAPRDHLARAFWQLRVSRAPTARRFARS -PSGDYLRALRACFLNDPARPRRGYEKFLQKKSRGEDPLKRPDWKVKCAKPGADGSPGGRR -GAGEAGRGRLPRGVGPGPGAAAARGPAPPPSRRGAPRRGGRGAGARWQLRPGAAAGSRPG -SLALNLLLSGSLERGSALRGRPRGLLSAAGGLGAGAPGSSGGGGCGCSTHLFSSDDILVT -RKDTWIPVLLLGGSRRRGRRRRCSGSSSPAQTLAFPEAPGAAAGTGRGGNMERAGHARAQ -GPGGERAGGRREGRRPPGSPPAAPPPGRPQQEEKGARRGEGGPRGPGGGEVLTAAPAAAL -GVGPRLAPHTRSHTRSLALPEQGRRKFCGCAWTPHTRRATVAVARGPRRGSPGATRTTDL -PNSQPSRPHNASSTAPARSPTLGPSPAPRAPPLPLTGLAPRMRSSRRPRTRRRRWPHRPS -PSPWVPSPCDGAAGPSRDFGSGSGSGSGGSQAVDPEIRDRDRGTAGEGGREPRTHAEAAR -APGAARREEQVCARRARAAGASLVLAEVFPRIAHTTGRKRNGVNFVLIQRQLQFPYYNVI -FLIQKRFIRM* ->chr22_18 # 33002 # 33439 # -1 # ID=1_18;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.482 -MGSHNPALLCLSSRYYFYYKSPNNTITKWMHPNQRNSLSINVLASFTSQRTLPLPTVQWE -YHLMKWVSTHAILQLRKTFTVLPRHTREPQKPSSSLALKRCLNLQAKPSNNRSVRRHFWS -SNKPVSSPTVRSVKGRRPYSQAPYS* ->chr22_19 # 35349 # 35690 # 1 # ID=1_19;partial=00;start_type=TTG;rbs_motif=TAAAA;rbs_spacer=13bp;genetic_code=4;gc_cont=0.377 -MILWSSSSSLSEAQVLTIGKPLSEYAHIKDLIIFVLMLKNFSEAFILFFPSLHRKFTLPS -WEAKETFYSTMFLTSSWKLMLEMGVGVGDGGGCTEAAGGRDRISEALSLAFFE* ->chr22_20 # 35821 # 35934 # -1 # ID=1_20;partial=00;start_type=ATG;rbs_motif=TATAA;rbs_spacer=14bp;genetic_code=4;gc_cont=0.342 -MVYIVMQYSFLSLISNSQIWKGEILLGEGRYKYRVAT* ->chr22_21 # 37683 # 38231 # 1 # ID=1_21;partial=00;start_type=ATG;rbs_motif=TTA;rbs_spacer=15bp;genetic_code=4;gc_cont=0.499 -MISVFVFFFFRQSLTLLPRLECSGVILAHCSRRPPDSSDLPGSASQKAGITGACHHTQLI -FVFLVEMGVHHVGQAGLKLLTSGDLPASALPKCWDYRREPPCLAEIISFFIIAIACRYML -VVICKNVIERPGTVAHTGNPSTLGGWGGRITRSGVGDQPGQYGETPSLPKIQKLAGHSGG -HL* ->chr22_22 # 39452 # 40000 # -1 # ID=1_22;partial=01;start_type=Edge;rbs_motif=None;rbs_spacer=None;genetic_code=4;gc_cont=0.681 -RPREGAGDPGLHPLLAVTLRPHDLEGLGMRGSLNLRRERGSGDLQGWAVGGCSEKLGRPA -GRICQFAQSALGARAEGGRRCRVPRDAPERAGASWKRPKQCVWTGIPRKQWPGRSTPAGQ -RARLRDRRRGWASPRTPTRARWLPRVPKNLSPGVLGRLLIPEQGCTGLHFLDVCDKVAFS -LL* diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap deleted file mode 100644 index 782d8c7..0000000 --- a/tests/main.nf.test.snap +++ /dev/null @@ -1,98 +0,0 @@ -{ - "Parameters: default": { - "content": [ - [ - [ - [ - "test1.viromeqc.tsv:md5,86a186c8212323e36c5c6e0aae844648", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" - ] - ] - ], - [ - [ - [ - "test1.fasta.gz:md5,eb5b39fab473c61e4e73802d0e1ef518", - "test2.fasta.gz:md5,eb5b39fab473c61e4e73802d0e1ef518" - ] - ] - ], - [ - [ - "test1.fasta_w_screen_hits.fna.gz:md5,e93c24be014c9bb221dc97caf118ad61", - "test2.fasta_w_screen_hits.fna.gz:md5,21a504e49b0bf3547604573aef34d6c1" - ], - [ - [ - "test1.screen:md5,b074c6861bab21e2b3aa63aebff1f392", - "test2.screen:md5,b074c6861bab21e2b3aa63aebff1f392" - ] - ] - ], - [ - [ - [ - [ - "all_samples_anicluster_representatives_virus.fna.gz:md5,07bf1a1918d0a5aa2422c7b1a3b1c085", - "all_samples_anicluster_representatives_virus_summary.tsv:md5,49535242cc88aebd1337c0d91e76e7f3" - ], - [ - "test1.fasta_w_screen_hits_virus.fna.gz:md5,3cc84b85ddcf944abd5a3a225b0ff404", - "test1.fasta_w_screen_hits_virus_summary.tsv:md5,791cd8249d24daf2dc3ea1f41aa3dba4" - ], - [ - "test2.fasta_w_screen_hits_virus.fna.gz:md5,3221973668db26d28b3fcf3113d03b37", - "test2.fasta_w_screen_hits_virus_summary.tsv:md5,617215f2a883d4ec8d95aacd0b09d8a1" - ] - ] - ] - ], - [ - [ - [ - [ - "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,494ecf2153a3316d7f975bcc045b3cd7" - ], - [ - "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,09b1e6883aac15f67d2f386661049166" - ] - ] - ], - [ - "test1.filtered.fna.gz:md5,c5f61c2d487959d8b2bda90adde5a44a", - "test2.filtered.fna.gz:md5,741ab7b127375e64069553fa51b2eac9" - ] - ], - [ - "all_samples_anicluster_representatives.fna.gz:md5,07bf1a1918d0a5aa2422c7b1a3b1c085", - [ - "all_samples_ani.tsv:md5,48b207f848d113168b6fb419d037731a" - ], - [ - "all_samples_clusters.tsv:md5,1011f14e48fa1e74f68126345741cafb", - "versions.yml:md5,68070b01cdc8bf2e8ea2eb4b97d2cdad" - ] - ], - "test1.bowtie2.log:md5,e7275c6347e7901c9bbb6ae4b317fcc1", - [ - [ - "all_samples_anicluster_representatives.fna.1.bt2:md5,2d27b4e32ccc71f6f7788dcef2aff18e", - "all_samples_anicluster_representatives.fna.2.bt2:md5,ba6e4f623336917cb116c4632a6b0f82", - "all_samples_anicluster_representatives.fna.3.bt2:md5,bc9a6e64bb55dfda29b4d8c18be153f1", - "all_samples_anicluster_representatives.fna.4.bt2:md5,334c5e3e240a27fa3e942c891e1fc6c5", - "all_samples_anicluster_representatives.fna.rev.1.bt2:md5,c55ba4fc2275e2a5bc0638b55cdf2474", - "all_samples_anicluster_representatives.fna.rev.2.bt2:md5,dfd26c60bd10b1e376c9a0357576eb30" - ] - ], - [ - "Host_prediction_to_genus_m90.csv:md5,528dcefb6a6c743b43f0dbc40bec3692" - ], - "test1.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135", - "test2.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135", - "software_versions.yml:md5,4fc2cd8b3cafaee61184a336efba386e" - ], - "timestamp": "2024-01-18T14:21:14.502195995" - } -} diff --git a/workflows/phageannotator/main.nf b/workflows/phageannotator/main.nf index 13478c3..3b7e488 100644 --- a/workflows/phageannotator/main.nf +++ b/workflows/phageannotator/main.nf @@ -47,7 +47,6 @@ include { BOWTIE2_BUILD } from '../../modules/nf-core/bo include { GENOMAD_ENDTOEND as GENOMAD_TAXONOMY } from '../../modules/nf-core/genomad/endtoend/main' include { GUNZIP as GUNZIP_CLUSTER_REPS } from '../../modules/nf-core/gunzip/main' include { GUNZIP as GUNZIP_VIRUS_PROTEINS } from '../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_VIRUS_GFF } from '../../modules/nf-core/gunzip/main' include { BACPHLIP } from '../../modules/nf-core/bacphlip/main' // @@ -104,7 +103,6 @@ workflow PHAGEANNOTATOR { // create channel from params.reference_virus_fasta ch_reference_virus_fasta_gz = Channel.value([ [ id:'reference_viruses' ], file( params.reference_virus_fasta, checkIfExists:true ) ]) - ch_reference_virus_fasta_gz // create channel from params.reference_virus_sketch if ( !params.reference_virus_sketch ){ @@ -336,19 +334,6 @@ workflow PHAGEANNOTATOR { /*---------------------------------------------------------------------------- Phage functional annotation ------------------------------------------------------------------------------*/ - if ( !params.skip_prodigalgv ) { - ch_prodigalgv_proteins_fna_gz = PRODIGAL_PRODIGALGV ( ch_anicluster_reps_fasta ).fna - ch_prodigalgv_proteins_faa_gz = PRODIGAL_PRODIGALGV.out.faa - ch_versions = ch_versions.mix( PRODIGAL_PRODIGALGV.out.versions ) - } else { - ch_prodigalgv_proteins_faa_gz = Channel.empty() - ch_prodigalgv_proteins_gff_gz = Channel.empty() - } - - // gunzip fasta for input into iphop, bacphlip, pharokka, - ch_prodigalgv_proteins_faa = GUNZIP_VIRUS_GFF ( ch_prodigalgv_proteins_faa_gz ).gunzip - ch_versions = ch_versions.mix( GUNZIP_VIRUS_GFF.out.versions ) - if ( !params.skip_pharokka ) { // create channel from params.pharokka_db if ( !params.pharokka_db ){ @@ -360,11 +345,12 @@ workflow PHAGEANNOTATOR { // // SUBWORKFLOW: Functionally annotate phage sequences // - ch_pharokka_ffn_gz = FASTA_PHAGE_FUNCTION_PHAROKKA ( ch_prodigalgv_proteins_faa, ch_pharokka_db ).pharokka_ffn_gz + ch_pharokka_gbk_gz = FASTA_PHAGE_FUNCTION_PHAROKKA ( ch_anicluster_reps_fasta, ch_pharokka_db ).pharokka_gbk_gz ch_pharokka_output_tsv = FASTA_PHAGE_FUNCTION_PHAROKKA.out.pharokka_final_output_tsv ch_versions = ch_versions.mix( FASTA_PHAGE_FUNCTION_PHAROKKA.out.versions ) } else { - ch_prodigalgv_proteins_fna_gz = Channel.empty() + ch_pharokka_gbk_gz = Channel.empty() + ch_pharokka_output_tsv = Channel.empty() } @@ -372,9 +358,26 @@ workflow PHAGEANNOTATOR { Analyze phage microdiversity ------------------------------------------------------------------------------*/ // gunzip proteins for input into instrain - ch_prodigalgv_proteins_fna = GUNZIP_VIRUS_PROTEINS ( ch_prodigalgv_proteins_fna_gz ).gunzip + ch_pharokka_gbk = GUNZIP_VIRUS_PROTEINS ( ch_pharokka_gbk_gz ).gunzip ch_versions = ch_versions.mix( GUNZIP_VIRUS_PROTEINS.out.versions ) + // add gene identifier to gbk for inStrain + ch_pharokka_gbk_mod = ch_pharokka_gbk + .map { meta, gbk -> + def gbk_mod = file("${workDir}/${meta.id}_mod.gbk") + + gbk.withReader { source -> + gbk_mod.withWriter { target -> + String line + while( line=source.readLine() ) { + target << line.replaceAll('/ID=','/gene=') << '\n' + } + } + } + + return [ meta, gbk_mod] + } + if ( !params.skip_instrain ) { // // MODULE: Generate instrain scaffold to bin file @@ -385,7 +388,7 @@ workflow PHAGEANNOTATOR { // // SUBWORKFLOW: Assess virus microdiversity within and across samples // - ch_gene_info_tsv = FASTA_MICRODIVERSITY_INSTRAIN ( ch_cluster_rep_alignment_bam, ch_anicluster_reps_fasta, ch_prodigalgv_proteins_fna, ch_stb_file_tsv ).gene_info_tsv + ch_gene_info_tsv = FASTA_MICRODIVERSITY_INSTRAIN ( ch_cluster_rep_alignment_bam, ch_anicluster_reps_fasta, ch_pharokka_gbk_mod, ch_stb_file_tsv ).gene_info_tsv ch_versions = ch_versions = ch_versions.mix(FASTA_MICRODIVERSITY_INSTRAIN.out.versions) } else { ch_gene_info_tsv = Channel.empty() diff --git a/workflows/phageannotator/nextflow.config b/workflows/phageannotator/nextflow.config index 913dfb3..89e17c9 100644 --- a/workflows/phageannotator/nextflow.config +++ b/workflows/phageannotator/nextflow.config @@ -7,7 +7,6 @@ includeConfig '../../modules/nf-core/cat/cat/nextflow.config' includeConfig '../../subworkflows/local/fasta_virus_classification_genomad/nextflow.config' includeConfig '../../subworkflows/local/fasta_virus_quality_checkv/nextflow.config' includeConfig '../../modules/local/qualityfilterviruses/nextflow.config' -includeConfig '../../modules/nf-core/custom/dumpsoftwareversions/nextflow.config' includeConfig '../../modules/nf-core/multiqc/nextflow.config' includeConfig '../../subworkflows/local/fasta_all_v_all_blast/nextflow.config' includeConfig '../../subworkflows/nf-core/bam_sort_stats_samtools/nextflow.config' diff --git a/workflows/phageannotator/tests/main.nf.test b/workflows/phageannotator/tests/main.nf.test index bdfbd06..a102999 100644 --- a/workflows/phageannotator/tests/main.nf.test +++ b/workflows/phageannotator/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/main.nf.test.snap b/workflows/phageannotator/tests/main.nf.test.snap index 7368b45..4f70f57 100644 --- a/workflows/phageannotator/tests/main.nf.test.snap +++ b/workflows/phageannotator/tests/main.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -73,10 +83,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -85,28 +111,38 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -140,7 +176,18 @@ ] ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "marker_taxonomy_tsv": [ [ @@ -151,7 +198,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -160,28 +212,38 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -199,8 +261,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -218,6 +290,6 @@ ] } ], - "timestamp": "2024-01-23T16:33:04.505262179" + "timestamp": "2024-01-31T15:39:29.234720854" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_bacphlip.nf.test b/workflows/phageannotator/tests/skip_bacphlip.nf.test index 29d1bdb..262c942 100644 --- a/workflows/phageannotator/tests/skip_bacphlip.nf.test +++ b/workflows/phageannotator/tests/skip_bacphlip.nf.test @@ -7,7 +7,7 @@ nextflow_workflow { tag "phageannotator" tag "phageannotator_skip_bacphlip" - test("Parameters: default") { + test("Parameters: skip_bacphlip = true") { when { workflow { """ @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap index 95f034e..fcc3dfd 100644 --- a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap +++ b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap @@ -1,10 +1,20 @@ { - "Parameters: default": { + "Parameters: skip_bacphlip = true": { "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -73,10 +83,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -85,27 +111,37 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -139,7 +175,18 @@ ] ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "marker_taxonomy_tsv": [ [ @@ -150,7 +197,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -159,27 +211,37 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -197,8 +259,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -216,6 +288,6 @@ ] } ], - "timestamp": "2024-01-23T16:45:40.239742787" + "timestamp": "2024-02-01T09:34:07.044453809" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_checkv.nf.test b/workflows/phageannotator/tests/skip_checkv.nf.test index 3b7b760..12772fb 100644 --- a/workflows/phageannotator/tests/skip_checkv.nf.test +++ b/workflows/phageannotator/tests/skip_checkv.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_checkv.nf.test.snap b/workflows/phageannotator/tests/skip_checkv.nf.test.snap index 79a718f..d811708 100644 --- a/workflows/phageannotator/tests/skip_checkv.nf.test.snap +++ b/workflows/phageannotator/tests/skip_checkv.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -62,10 +72,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,b4c05c312e5bf4a3e01e0fa599472982" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,829d648756f80789738e5be6328c699f" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,829d648756f80789738e5be6328c699f" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -73,27 +99,37 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", 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"versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -127,7 +163,18 @@ ] ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,829d648756f80789738e5be6328c699f" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,829d648756f80789738e5be6328c699f" + ] ], "marker_taxonomy_tsv": [ [ @@ -138,7 +185,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,b4c05c312e5bf4a3e01e0fa599472982" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -146,27 +198,37 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -184,14 +246,24 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ ] } ], - "timestamp": "2024-01-23T16:37:32.945792353" + "timestamp": "2024-02-01T09:53:35.649543801" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test b/workflows/phageannotator/tests/skip_genomad.nf.test index 94ab3f9..2cea701 100644 --- a/workflows/phageannotator/tests/skip_genomad.nf.test +++ b/workflows/phageannotator/tests/skip_genomad.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test.snap b/workflows/phageannotator/tests/skip_genomad.nf.test.snap index 09ea708..d110fee 100644 --- a/workflows/phageannotator/tests/skip_genomad.nf.test.snap +++ b/workflows/phageannotator/tests/skip_genomad.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ @@ -62,10 +72,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + 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b/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap b/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap index 4a129de..23938ee 100644 --- a/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap +++ b/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -68,10 +78,26 @@ ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -80,27 +106,37 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", 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"test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -206,6 +278,6 @@ ] } ], - "timestamp": "2024-01-23T16:08:46.939222078" + "timestamp": "2024-02-01T10:12:35.131972876" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_instrain.nf.test b/workflows/phageannotator/tests/skip_instrain.nf.test index 9768ac0..f11cd45 100644 --- a/workflows/phageannotator/tests/skip_instrain.nf.test +++ b/workflows/phageannotator/tests/skip_instrain.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_instrain.nf.test.snap b/workflows/phageannotator/tests/skip_instrain.nf.test.snap index 23a1804..9154167 100644 --- a/workflows/phageannotator/tests/skip_instrain.nf.test.snap +++ b/workflows/phageannotator/tests/skip_instrain.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - 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"versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -150,7 +172,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -159,10 +186,13 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", @@ -173,13 +203,17 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -197,8 +231,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -216,6 +260,6 @@ ] } ], - "timestamp": "2024-01-23T15:53:05.450284991" + "timestamp": "2024-02-01T11:21:22.84592657" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_iphop.nf.test b/workflows/phageannotator/tests/skip_iphop.nf.test index 18ae03b..3ab7a00 100644 --- a/workflows/phageannotator/tests/skip_iphop.nf.test +++ b/workflows/phageannotator/tests/skip_iphop.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_iphop.nf.test.snap b/workflows/phageannotator/tests/skip_iphop.nf.test.snap index a122b22..6d11f4e 100644 --- a/workflows/phageannotator/tests/skip_iphop.nf.test.snap +++ b/workflows/phageannotator/tests/skip_iphop.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -68,10 +78,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -79,26 +105,36 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -127,7 +163,18 @@ ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "marker_taxonomy_tsv": [ [ @@ -138,7 +185,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -146,26 +198,36 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -183,8 +245,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -202,6 +274,6 @@ ] } ], - "timestamp": "2024-01-23T16:41:16.98960274" + "timestamp": "2024-02-01T11:51:49.427932984" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_pharokka.nf.test b/workflows/phageannotator/tests/skip_pharokka.nf.test index 886277f..36fb384 100644 --- a/workflows/phageannotator/tests/skip_pharokka.nf.test +++ b/workflows/phageannotator/tests/skip_pharokka.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_pharokka.nf.test.snap b/workflows/phageannotator/tests/skip_pharokka.nf.test.snap index 8157c1c..88cc79d 100644 --- a/workflows/phageannotator/tests/skip_pharokka.nf.test.snap +++ b/workflows/phageannotator/tests/skip_pharokka.nf.test.snap @@ -1,10 +1,20 @@ { - "Parameters: skip_prodigalgv = true": { + "Parameters: skip_pharokka = true": { "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -81,6 +91,7 @@ "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", @@ -97,7 +108,6 @@ "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", - "versions.yml:md5,78b447897aac9e6a891f06a6c4af0e99", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", @@ -111,8 +121,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ [ @@ -155,12 +164,13 @@ "all_samples_anicluster_representatives_taxonomy.tsv:md5,fb8440b1fd32f96414b71b76ec228df1" ] ], - "prodigalgv_proteins_faa_gz": [ + "pharokka_output_tsv": [ ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", + "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", @@ -177,7 +187,6 @@ "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", - "versions.yml:md5,78b447897aac9e6a891f06a6c4af0e99", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", @@ -191,8 +200,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", - "versions.yml:md5,fc95484076ab0130345b4f7ab7f2e37a" + "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ [ @@ -209,8 +217,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -228,6 +246,6 @@ ] } ], - "timestamp": "2024-01-01T11:24:18.549182697" + "timestamp": "2024-02-01T13:49:47.785546294" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_reference_containment.nf.test b/workflows/phageannotator/tests/skip_reference_containment.nf.test index ba662d0..d1efd59 100644 --- a/workflows/phageannotator/tests/skip_reference_containment.nf.test +++ b/workflows/phageannotator/tests/skip_reference_containment.nf.test @@ -17,8 +17,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap index 41d4232..f761ed9 100644 --- a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap +++ b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -73,10 +83,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,8080e1ffca88bbda0401ec61bafb9d30" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,e20016bcf7dbe097ef5c3df924e4c3c8" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,e20016bcf7dbe097ef5c3df924e4c3c8" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -84,27 +110,37 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -138,7 +174,18 @@ ] ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,e20016bcf7dbe097ef5c3df924e4c3c8" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,e20016bcf7dbe097ef5c3df924e4c3c8" + ] ], "marker_taxonomy_tsv": [ [ @@ -149,7 +196,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,8080e1ffca88bbda0401ec61bafb9d30" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -157,27 +209,37 @@ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -195,8 +257,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -214,6 +286,6 @@ ] } ], - "timestamp": "2024-01-23T16:19:56.384052704" + "timestamp": "2024-02-01T14:08:46.916902313" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_viromeqc.nf.test b/workflows/phageannotator/tests/skip_viromeqc.nf.test index e07f441..6054e14 100644 --- a/workflows/phageannotator/tests/skip_viromeqc.nf.test +++ b/workflows/phageannotator/tests/skip_viromeqc.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap index 8b06274..b4c696c 100644 --- a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap +++ b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap @@ -72,10 +72,26 @@ ] ], "7": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "8": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "9": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -84,26 +100,36 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -137,7 +163,18 @@ ] ], "instrain_gene_info": [ - + [ + { + "id": "test2" + }, + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ], + [ + { + "id": "test" + }, + "test.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b" + ] ], "marker_taxonomy_tsv": [ [ @@ -148,7 +185,12 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "all_samples" + }, + "all_samples_cds_final_merged_output.tsv:md5,082c9a1097ca95af4cf4e3fe9f6ededb" + ] ], "versions": [ "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", @@ -157,26 +199,36 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", + "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -212,6 +264,6 @@ ] } ], - "timestamp": "2024-01-23T16:50:43.307880674" + "timestamp": "2024-02-01T15:00:37.195786662" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_virus_clustering.nf.test b/workflows/phageannotator/tests/skip_virus_clustering.nf.test index 91a7342..72de4a6 100644 --- a/workflows/phageannotator/tests/skip_virus_clustering.nf.test +++ b/workflows/phageannotator/tests/skip_virus_clustering.nf.test @@ -15,8 +15,8 @@ nextflow_workflow { file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ], [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true), file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists:true) ] ] ) - input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ], - [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['contigs_fa_gz'], checkIfExists:true) ] ]) + input[1] = Channel.of( [ [ id:'test' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ], + [ [ id:'test2' ], [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists:true) ] ]) """ } params { diff --git a/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap b/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap index fba5ef7..3cd5879 100644 --- a/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap +++ b/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap @@ -3,8 +3,18 @@ "content": [ { "0": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "1": [ [ @@ -91,7 +101,18 @@ ] ], "7": [ - + [ + { + "id": "test2" + }, + "test2_cds_final_merged_output.tsv:md5,ec0ed1086d239db645779da72b713f6c" + ], + [ + { + "id": "test" + }, + "test_cds_final_merged_output.tsv:md5,4b3fbda61d1af94fed989c70fde8088b" + ] ], "8": [ @@ -102,12 +123,15 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", @@ -115,15 +139,18 @@ "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -187,7 +214,18 @@ ] ], "pharokka_output_tsv": [ - + [ + { + "id": "test2" + }, + "test2_cds_final_merged_output.tsv:md5,ec0ed1086d239db645779da72b713f6c" + ], + [ + { + "id": "test" + }, + "test_cds_final_merged_output.tsv:md5,4b3fbda61d1af94fed989c70fde8088b" + ] ], "versions": [ "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", @@ -195,12 +233,15 @@ "versions.yml:md5,1097ac7d62d13e9e74916d9dc1fabb7b", "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", + "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", - "versions.yml:md5,45fa41ba465519ccbfe26974f9aebcc4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", + "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", + "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", @@ -208,15 +249,18 @@ "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", + "versions.yml:md5,987d2e54a85311b917599dc41c90418c", + "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", + "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", + "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", - "versions.yml:md5,e70dcabc3ee5ee42a1800b07fdfd90fd", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -235,8 +279,18 @@ ] ], "virus_enrichment_tsv": [ - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae", - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + [ + { + "id": "test2" + }, + "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" + ], + [ + { + "id": "test" + }, + "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" + ] ], "virus_quality_tsv": [ [ @@ -254,6 +308,6 @@ ] } ], - "timestamp": "2024-01-23T16:15:10.435647908" + "timestamp": "2024-02-01T15:21:27.006208845" } } \ No newline at end of file From 58abc09bc1a2479d85d7a33837a855104e07bd9f Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 8 Feb 2024 15:02:29 -0800 Subject: [PATCH 04/23] Fixed linting and reorganized test_data --- conf/test.config | 6 +- .../local/prodigal/prodigalgv/environment.yml | 6 -- modules/local/prodigal/prodigalgv/main.nf | 54 ----------- .../local/prodigal/prodigalgv/nextflow.config | 10 -- .../prodigal/prodigalgv/tests/main.nf.test | 55 ----------- .../prodigalgv/tests/main.nf.test.snap | 92 ------------------- .../local/prodigal/prodigalgv/tests/tags.yml | 2 - .../nf-core/checkv/downloaddatabase/main.nf | 2 - modules/nf-core/genomad/download/main.nf | 2 - nextflow.config | 2 - nextflow_schema.json | 17 ++-- nf-test.config | 12 +-- workflows/phageannotator/main.nf | 1 - 13 files changed, 16 insertions(+), 245 deletions(-) delete mode 100644 modules/local/prodigal/prodigalgv/environment.yml delete mode 100644 modules/local/prodigal/prodigalgv/main.nf delete mode 100644 modules/local/prodigal/prodigalgv/nextflow.config delete mode 100644 modules/local/prodigal/prodigalgv/tests/main.nf.test delete mode 100644 modules/local/prodigal/prodigalgv/tests/main.nf.test.snap delete mode 100644 modules/local/prodigal/prodigalgv/tests/tags.yml diff --git a/conf/test.config b/conf/test.config index afd97ff..36581af 100644 --- a/conf/test.config +++ b/conf/test.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function ' // Limit resources so that this can run on GitHub Actions - //max_cpus = 2 - //max_memory = '6.GB' + max_cpus = 2 + max_memory = '6.GB' max_time = '6.h' // Input data @@ -30,3 +30,5 @@ params { // Pipeline options publish_dir_mode = 'symlink' } + +includeConfig 'conf/test_data.config' diff --git a/modules/local/prodigal/prodigalgv/environment.yml b/modules/local/prodigal/prodigalgv/environment.yml deleted file mode 100644 index 2bbcbb2..0000000 --- a/modules/local/prodigal/prodigalgv/environment.yml +++ /dev/null @@ -1,6 +0,0 @@ -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::prodigal-gv=2.11.0 diff --git a/modules/local/prodigal/prodigalgv/main.nf b/modules/local/prodigal/prodigalgv/main.nf deleted file mode 100644 index fa04acf..0000000 --- a/modules/local/prodigal/prodigalgv/main.nf +++ /dev/null @@ -1,54 +0,0 @@ -process PRODIGAL_PRODIGALGV { - tag "$meta.id" - label 'process_high' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/prodigal-gv:2.11.0--he4a0461_2': - 'biocontainers/prodigal-gv:2.11.0--he4a0461_2' }" - - input: - tuple val(meta), path(fasta) - - output: - tuple val(meta), path("*.prodigalgv.faa.gz") , emit: faa - tuple val(meta), path("*.prodigalgv.fna.gz") , emit: fna - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - prodigal-gv \\ - -i $fasta \\ - -d ${prefix}.prodigalgv.fna \\ - -a ${prefix}.prodigalgv.faa \\ - $args - - gzip ${prefix}.prodigalgv.fna - gzip ${prefix}.prodigalgv.faa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - prodigalgv: \$(echo \$(prodigal-gv --version 2>&1) | awk 'NF{ print \$NF }') - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.prodigalgv.fna - gzip ${prefix}.prodigalgv.fna - touch ${prefix}.prodigalgv.faa - gzip ${prefix}.prodigalgv.faa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - prodigalgv: \$(echo \$(prodigal-gv --version 2>&1) | awk 'NF{ print \$NF }') - END_VERSIONS - """ -} diff --git a/modules/local/prodigal/prodigalgv/nextflow.config b/modules/local/prodigal/prodigalgv/nextflow.config deleted file mode 100644 index fb712df..0000000 --- a/modules/local/prodigal/prodigalgv/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - withName: PRODIGAL_PRODIGALGV { - publishDir = [ - path: { "${params.outdir}/GenePrediction/prodigal/prodigalgv" }, - mode: params.publish_dir_mode, - pattern: '*.prodigalgv.f*a.gz', - ] - ext.args = "-p meta" - } -} diff --git a/modules/local/prodigal/prodigalgv/tests/main.nf.test b/modules/local/prodigal/prodigalgv/tests/main.nf.test deleted file mode 100644 index 053f515..0000000 --- a/modules/local/prodigal/prodigalgv/tests/main.nf.test +++ /dev/null @@ -1,55 +0,0 @@ -nextflow_process { - - name "Test Process: PRODIGAL_PRODIGALGV" - script "../main.nf" - process "PRODIGAL_PRODIGALGV" - tag "modules" - tag "modules_local" - tag "prodigal" - tag "prodigal/prodigalgv" - - - test("['sarscov2']['genome']['genome_fasta']") { - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = [ [ id: 'all_samples' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("['sarscov2']['genome']['genome_fasta'] - stub") { - - options "-stub" - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = [ [ id: 'all_samples' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap b/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap deleted file mode 100644 index efaa6de..0000000 --- a/modules/local/prodigal/prodigalgv/tests/main.nf.test.snap +++ /dev/null @@ -1,92 +0,0 @@ -{ - "['sarscov2']['genome']['genome_fasta']": { - "content": [ - { - "0": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,df108523d0141cb4cec62a09e2646348" - ] - ], - "1": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.fna.gz:md5,c2a99be1dfbcea362f0e0ece02e7c0a6" - ] - ], - "2": [ - "versions.yml:md5,3849079cb0a073e302ead9d90e4624d4" - ], - "faa": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,df108523d0141cb4cec62a09e2646348" - ] - ], - "fna": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.fna.gz:md5,c2a99be1dfbcea362f0e0ece02e7c0a6" - ] - ], - "versions": [ - "versions.yml:md5,3849079cb0a073e302ead9d90e4624d4" - ] - } - ], - "timestamp": "2024-01-24T13:41:31.810729686" - }, - "['sarscov2']['genome']['genome_fasta'] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,3849079cb0a073e302ead9d90e4624d4" - ], - "faa": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.faa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fna": [ - [ - { - "id": "all_samples" - }, - "all_samples.prodigalgv.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,3849079cb0a073e302ead9d90e4624d4" - ] - } - ], - "timestamp": "2024-01-24T13:41:41.320396288" - } -} \ No newline at end of file diff --git a/modules/local/prodigal/prodigalgv/tests/tags.yml b/modules/local/prodigal/prodigalgv/tests/tags.yml deleted file mode 100644 index 7155aeb..0000000 --- a/modules/local/prodigal/prodigalgv/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -prodigal/prodigalgv: - - modules/local/prodigal/prodigalgv/** diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index 2043d55..bc5086f 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,8 +18,6 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index 632d494..a2ac6ec 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,8 +16,6 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy genomad \\ download-database . diff --git a/nextflow.config b/nextflow.config index 46650cd..0673161 100644 --- a/nextflow.config +++ b/nextflow.config @@ -248,8 +248,6 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -includeConfig 'conf/test_data.config' - // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Singularity are enabled // Set to your registry if you have a mirror of containers diff --git a/nextflow_schema.json b/nextflow_schema.json index 17e5610..1601234 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -296,15 +296,17 @@ } } }, - "virus_gene_prediction": { - "title": "Virus gene prediction", + "virus_function_options": { + "title": "Virus function options", "type": "object", - "description": "Predict ORFs contained in viral sequences", + "description": "Functionally annotate viral genomes using a variety of approaches", "default": "", "properties": { - "skip_prodigalgv": { - "type": "boolean", - "description": "Skip running Prodigal-gv to predict ORFs in viral sequences" + "skip_pharokka": { + "type": "boolean" + }, + "pharokka_db": { + "type": "string" } } }, @@ -376,7 +378,6 @@ }, "genomad_sensitivity": { "type": "number", - "default": 4.2, "hidden": true }, "checkv_minimal_db": { @@ -624,7 +625,7 @@ "$ref": "#/definitions/virus_lifestyle_options" }, { - "$ref": "#/definitions/virus_gene_prediction" + "$ref": "#/definitions/virus_function_options" }, { "$ref": "#/definitions/virus_microdiversity_options" diff --git a/nf-test.config b/nf-test.config index d97921a..3ba80fb 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,16 +1,10 @@ config { - // location for all nf-tests + // Location of nf-tests testsDir "." - // nf-test directory including temporary files for each test - workDir ".nf-tests/" - - // location of library folder that is added automatically to the classpath - libDir "lib/" + // nf-test directory used to create temporary files for each test + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests configFile "nextflow.config" - - // run all test with the defined docker profile from the main nextflow.config - profile "" } diff --git a/workflows/phageannotator/main.nf b/workflows/phageannotator/main.nf index 3b7e488..10ab164 100644 --- a/workflows/phageannotator/main.nf +++ b/workflows/phageannotator/main.nf @@ -17,7 +17,6 @@ include { ANICLUSTER_ANICALC } from '../../modules/local/ include { ANICLUSTER_ANICLUST } from '../../modules/local/anicluster/aniclust/main' include { ANICLUSTER_EXTRACTREPS } from '../../modules/local/anicluster/extractreps/main' include { COVERM_CONTIG } from '../../modules/local/coverm/contig/main' // TODO: Add to nf-core -include { PRODIGAL_PRODIGALGV } from '../../modules/local/prodigal/prodigalgv/main' // TODO: Add to nf-core include { INSTRAIN_STB } from '../../modules/local/instrain/stb/main' // From 42a07940aeea7f9f6ab6d4b1547ee37b6e9078a3 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 8 Feb 2024 15:05:23 -0800 Subject: [PATCH 05/23] Removed prodigal/prodigalgv nextlfow.config --- workflows/phageannotator/nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/phageannotator/nextflow.config b/workflows/phageannotator/nextflow.config index 89e17c9..e52ab6c 100644 --- a/workflows/phageannotator/nextflow.config +++ b/workflows/phageannotator/nextflow.config @@ -16,7 +16,6 @@ includeConfig '../../modules/local/coverm/contig/nextflow.config' includeConfig '../../subworkflows/local/fasta_phage_host_iphop/nextflow.config' includeConfig '../../modules/nf-core/gunzip/nextflow.config' includeConfig '../../modules/nf-core/bacphlip/nextflow.config' -includeConfig '../../modules/local/prodigal/prodigalgv/nextflow.config' includeConfig '../../subworkflows/local/fasta_phage_function_pharokka/nextflow.config' includeConfig '../../modules/local/instrain/stb/nextflow.config' includeConfig '../../subworkflows/local/fasta_microdiversity_instrain/nextflow.config' From 04684ca0a6cdcda1b901cf8aaf9310868093ec6c Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 8 Feb 2024 15:15:11 -0800 Subject: [PATCH 06/23] Fixed test_data, patched pharokka, and updated samtools/sort --- conf/test.config | 2 +- modules.json | 5 +- .../pharokka/pharokka/pharokka-pharokka.diff | 73 +++++++++++++++++++ modules/nf-core/samtools/sort/environment.yml | 4 +- modules/nf-core/samtools/sort/main.nf | 4 +- modules/nf-core/samtools/sort/nextflow.config | 5 -- .../nf-core/samtools/sort/tests/main.nf.test | 5 +- .../samtools/sort/tests/main.nf.test.snap | 48 +++--------- .../samtools/sort/tests/nextflow.config | 2 + 9 files changed, 98 insertions(+), 50 deletions(-) create mode 100644 modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff delete mode 100644 modules/nf-core/samtools/sort/nextflow.config diff --git a/conf/test.config b/conf/test.config index 36581af..c8b4628 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,4 +31,4 @@ params { publish_dir_mode = 'symlink' } -includeConfig 'conf/test_data.config' +includeConfig './test_data.config' diff --git a/modules.json b/modules.json index 7e062da..e4c4180 100644 --- a/modules.json +++ b/modules.json @@ -120,7 +120,8 @@ "pharokka/pharokka": { "branch": "master", "git_sha": "10e88ef2f1f3ff012a2c9562de95c264006ebf21", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff" }, "samtools/flagstat": { "branch": "master", @@ -139,7 +140,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { diff --git a/modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff b/modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff new file mode 100644 index 0000000..aebb281 --- /dev/null +++ b/modules/nf-core/pharokka/pharokka/pharokka-pharokka.diff @@ -0,0 +1,73 @@ +Changes in module 'nf-core/pharokka/pharokka' +--- /dev/null ++++ modules/nf-core/pharokka/pharokka/nextflow.config +@@ -0,0 +1,12 @@ ++process { ++ withName: PHAROKKA_PHAROKKA { ++ ext.args = [ ++ "--meta", ++ ].join(' ').trim() ++ publishDir = [ ++ path: { "${params.outdir}/PhageFunction/pharokka/pharokka" }, ++ mode: params.publish_dir_mode, ++ pattern: '*', ++ ] ++ } ++} +--- modules/nf-core/pharokka/pharokka/main.nf ++++ modules/nf-core/pharokka/pharokka/main.nf +@@ -12,14 +12,15 @@ + path pharokka_db + + output: +- tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv") , emit: cds_final_merged_output +- tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_functions.tsv") , emit: cds_functions +- tuple val(meta), path("${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv") , emit: length_gc_cds_density +- tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_card.tsv") , emit: card , optional: true +- tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv") , emit: vfdb , optional: true +- tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv") , emit: mash , optional: true +- tuple val(meta), path("${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta") , emit: reoriented , optional: true +- path "versions.yml" , emit: versions ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv") , emit: cds_final_merged_output ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_cds_functions.tsv") , emit: cds_functions ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv") , emit: length_gc_cds_density ++ tuple val(meta), path("${prefix}_pharokka/${prefix}.gbk.gz") , emit: gbk ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_card.tsv") , emit: card , optional: true ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv") , emit: vfdb , optional: true ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv") , emit: mash , optional: true ++ tuple val(meta), path("${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta.gz") , emit: reoriented , optional: true ++ path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when +@@ -35,7 +36,9 @@ + --database ${pharokka_db} \\ + --threads ${task.cpus} \\ + --prefix ${prefix} \\ +- $args ++ $args ++ ++ gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff ${prefix}_pharokka/*.gbk + + cat <<-END_VERSIONS > versions.yml + "${task.process}": +@@ -49,6 +52,8 @@ + + """ + mkdir -p ${prefix}_pharokka ++ touch ${prefix}_pharokka/prodigal-gv.ffn ++ touch ${prefix}_pharokka/prodigal-gv.faa + touch ${prefix}_pharokka/${prefix}.gbk + touch ${prefix}_pharokka/${prefix}.log + touch ${prefix}_pharokka/${prefix}_cds_functions.tsv +@@ -57,6 +62,8 @@ + touch ${prefix}_pharokka/${prefix}_top_hits_inphared + touch ${prefix}_pharokka/${prefix} + ++ gzip ${prefix}_pharokka/*.ffn ${prefix}_pharokka/*.faa ${prefix}_pharokka/*.gff ${prefix}_pharokka/*.gbk ++ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pharokka: \$(pharokka.py --version) + +************************************************************ diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 04c82f1..f4064b7 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,8 @@ +name: samtools_sort channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 + - bioconda::htslib=1.18 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 60f0c63..4a666d4 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/sort/nextflow.config b/modules/nf-core/samtools/sort/nextflow.config deleted file mode 100644 index d9b82e4..0000000 --- a/modules/nf-core/samtools/sort/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } - } -} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 1f72f3b..abb8097 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -61,7 +61,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() } ) } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 07fc610..ff72225 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "1": [ ], "2": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ], "bam": [ [ @@ -23,54 +23,26 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "csi": [ ], "versions": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ] } ], - "timestamp": "2023-10-17T17:21:46.5427968" + "timestamp": "2023-12-04T11:11:22.005628301" }, "test_samtools_sort_stub": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" - ] - } + "test.sorted.bam", + [ + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + ] ], - "timestamp": "2024-01-30T15:07:33.996526252" + "timestamp": "2023-12-04T17:47:22.314445935" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config index d2a119b..d0f3508 100644 --- a/modules/nf-core/samtools/sort/tests/nextflow.config +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -1,5 +1,7 @@ process { + withName: SAMTOOLS_SORT { ext.prefix = { "${meta.id}.sorted" } } + } From 7406a89eac975b632d6ae8c531182028123112e7 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 8 Feb 2024 15:17:11 -0800 Subject: [PATCH 07/23] Added samtools/sort nextlfow.config --- modules/nf-core/samtools/sort/nextflow.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 modules/nf-core/samtools/sort/nextflow.config diff --git a/modules/nf-core/samtools/sort/nextflow.config b/modules/nf-core/samtools/sort/nextflow.config new file mode 100644 index 0000000..e69de29 From ada963ee01a1b57e8dfc787462616cc2d5a7df2c Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 8 Feb 2024 15:54:57 -0800 Subject: [PATCH 08/23] Fixed test_data include --- conf/test.config | 2 -- conf/test_data.config | 1 + nextflow.config | 2 ++ 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index c8b4628..2510ff2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,5 +30,3 @@ params { // Pipeline options publish_dir_mode = 'symlink' } - -includeConfig './test_data.config' diff --git a/conf/test_data.config b/conf/test_data.config index ce95684..2d4f56c 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -4,6 +4,7 @@ params { // Base directory for test data nf_core_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" + test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" phageannotator_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" modules_testdata_base_path = "s3://ngi-igenomes/testdata/nf-core/modules/" diff --git a/nextflow.config b/nextflow.config index 4acd300..a54dda2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -137,6 +137,8 @@ params { } +includeConfig 'conf/test_data.config' + // Load base.config by default for all pipelines includeConfig 'conf/base.config' From 04f4d2748816053849609e41d193483c20c255ac Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Mon, 12 Feb 2024 09:07:45 -0800 Subject: [PATCH 09/23] Added ext.prefix to disambiguate input/output names --- .../custom/dumpsoftwareversions/nextflow.config | 9 +++++++++ modules/nf-core/samtools/sort/nextflow.config | 5 +++++ tests/main.nf.test.snap | 10 +++++----- workflows/phageannotator/nextflow.config | 1 + workflows/phageannotator/tests/main.nf.test.snap | 10 +++++++--- 5 files changed, 27 insertions(+), 8 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/nextflow.config diff --git a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config new file mode 100644 index 0000000..055400d --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/nextflow.config b/modules/nf-core/samtools/sort/nextflow.config index e69de29..d9b82e4 100644 --- a/modules/nf-core/samtools/sort/nextflow.config +++ b/modules/nf-core/samtools/sort/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + } +} \ No newline at end of file diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index cb09524..be71653 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -89,14 +89,14 @@ [ "Host_prediction_to_genus_m90.csv:md5,528dcefb6a6c743b43f0dbc40bec3692" ], - "test1.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135", - "test2.IS_gene_info.tsv:md5,dd7c9eb0c52908beaf21b5fb9ec91135", - "software_versions.yml:md5,c355834117410512c963268dc0d073a4" + "test1.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", + "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", + "software_versions.yml:md5,d6a63054b92c6bd4cda093b3592e81e1" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-06T10:51:33.932290548" + "timestamp": "2024-02-09T13:37:29.504208615" } -} +} \ No newline at end of file diff --git a/workflows/phageannotator/nextflow.config b/workflows/phageannotator/nextflow.config index e52ab6c..4431fe8 100644 --- a/workflows/phageannotator/nextflow.config +++ b/workflows/phageannotator/nextflow.config @@ -19,3 +19,4 @@ includeConfig '../../modules/nf-core/bacphlip/nextflow.config' includeConfig '../../subworkflows/local/fasta_phage_function_pharokka/nextflow.config' includeConfig '../../modules/local/instrain/stb/nextflow.config' includeConfig '../../subworkflows/local/fasta_microdiversity_instrain/nextflow.config' +includeConfig '../../modules/nf-core/custom/dumpsoftwareversions/nextflow.config' diff --git a/workflows/phageannotator/tests/main.nf.test.snap b/workflows/phageannotator/tests/main.nf.test.snap index 4f70f57..43c83ce 100644 --- a/workflows/phageannotator/tests/main.nf.test.snap +++ b/workflows/phageannotator/tests/main.nf.test.snap @@ -133,7 +133,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -143,6 +142,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -234,7 +234,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -244,6 +243,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -290,6 +290,10 @@ ] } ], - "timestamp": "2024-01-31T15:39:29.234720854" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-09T15:49:14.848581359" } } \ No newline at end of file From 5695662e3df32201fe8ff9d8228d98519ede283e Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Mon, 12 Feb 2024 15:57:12 -0800 Subject: [PATCH 10/23] Started fixing nf-test snapshots --- conf/test.config | 4 ++-- modules/nf-core/checkv/downloaddatabase/main.nf | 2 ++ modules/nf-core/genomad/download/main.nf | 2 ++ .../phageannotator/tests/skip_bacphlip.nf.test.snap | 10 +++++++--- .../phageannotator/tests/skip_checkv.nf.test.snap | 10 +++++++--- .../phageannotator/tests/skip_genomad.nf.test.snap | 10 +++++++--- .../tests/skip_genomad_taxonomy.nf.test.snap | 10 +++++++--- .../phageannotator/tests/skip_instrain.nf.test.snap | 10 +++++++--- .../phageannotator/tests/skip_pharokka.nf.test.snap | 10 +++++++--- 9 files changed, 48 insertions(+), 20 deletions(-) diff --git a/conf/test.config b/conf/test.config index 2510ff2..afd97ff 100644 --- a/conf/test.config +++ b/conf/test.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function ' // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' + //max_cpus = 2 + //max_memory = '6.GB' max_time = '6.h' // Input data diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index bc5086f..2043d55 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,6 +18,8 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index a2ac6ec..632d494 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,6 +16,8 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy genomad \\ download-database . diff --git a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap index fcc3dfd..fa7f50f 100644 --- a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap +++ b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap @@ -132,7 +132,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -142,6 +141,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -232,7 +232,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -242,6 +241,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -288,6 +288,10 @@ ] } ], - "timestamp": "2024-02-01T09:34:07.044453809" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T10:13:55.648781029" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_checkv.nf.test.snap b/workflows/phageannotator/tests/skip_checkv.nf.test.snap index d811708..e8063f3 100644 --- a/workflows/phageannotator/tests/skip_checkv.nf.test.snap +++ b/workflows/phageannotator/tests/skip_checkv.nf.test.snap @@ -121,7 +121,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -130,6 +129,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -220,7 +220,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -229,6 +228,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -264,6 +264,10 @@ ] } ], - "timestamp": "2024-02-01T09:53:35.649543801" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T10:22:58.20948719" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test.snap b/workflows/phageannotator/tests/skip_genomad.nf.test.snap index d110fee..46ea832 100644 --- a/workflows/phageannotator/tests/skip_genomad.nf.test.snap +++ b/workflows/phageannotator/tests/skip_genomad.nf.test.snap @@ -122,7 +122,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -132,6 +131,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -223,7 +223,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -233,6 +232,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -268,6 +268,10 @@ ] } ], - "timestamp": "2024-02-01T10:47:39.555120734" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T10:55:05.591614887" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap b/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap index 23938ee..1c504cb 100644 --- a/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap +++ b/workflows/phageannotator/tests/skip_genomad_taxonomy.nf.test.snap @@ -128,7 +128,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -137,6 +136,7 @@ "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -223,7 +223,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -232,6 +231,7 @@ "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -278,6 +278,10 @@ ] } ], - "timestamp": "2024-02-01T10:12:35.131972876" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T11:44:28.164377694" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_instrain.nf.test.snap b/workflows/phageannotator/tests/skip_instrain.nf.test.snap index 9154167..bbab5f0 100644 --- a/workflows/phageannotator/tests/skip_instrain.nf.test.snap +++ b/workflows/phageannotator/tests/skip_instrain.nf.test.snap @@ -118,7 +118,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -128,6 +127,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -204,7 +204,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -214,6 +213,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -260,6 +260,10 @@ ] } ], - "timestamp": "2024-02-01T11:21:22.84592657" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T15:56:57.406989091" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_pharokka.nf.test.snap b/workflows/phageannotator/tests/skip_pharokka.nf.test.snap index 88cc79d..b4134af 100644 --- a/workflows/phageannotator/tests/skip_pharokka.nf.test.snap +++ b/workflows/phageannotator/tests/skip_pharokka.nf.test.snap @@ -112,7 +112,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -121,6 +120,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -191,7 +191,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -200,6 +199,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -246,6 +246,10 @@ ] } ], - "timestamp": "2024-02-01T13:49:47.785546294" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-12T09:49:38.200934849" } } \ No newline at end of file From fb20bffa621a87808a61d8691a3013dedc02eb93 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 14 Feb 2024 10:45:12 -0800 Subject: [PATCH 11/23] Fixed resource requests --- conf/test.config | 4 ++-- modules/nf-core/checkv/downloaddatabase/main.nf | 2 -- modules/nf-core/genomad/download/main.nf | 2 -- 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/conf/test.config b/conf/test.config index afd97ff..2510ff2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -15,8 +15,8 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function ' // Limit resources so that this can run on GitHub Actions - //max_cpus = 2 - //max_memory = '6.GB' + max_cpus = 2 + max_memory = '6.GB' max_time = '6.h' // Input data diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index 2043d55..bc5086f 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,8 +18,6 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index 632d494..a2ac6ec 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,8 +16,6 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy genomad \\ download-database . From 8da07c33498ddea1d98caf95876cbc2db6d47348 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 14 Feb 2024 12:47:20 -0800 Subject: [PATCH 12/23] Updated snapshots --- .github/workflows/ci.yml | 2 +- conf/test_data.config | 1214 ++++++++--------- nf-test.config | 2 +- .../tests/main.nf.test.snap | 12 +- tests/nextflow.config | 35 + .../tests/skip_iphop.nf.test.snap | 10 +- .../tests/skip_viromeqc.nf.test.snap | 10 +- 7 files changed, 665 insertions(+), 620 deletions(-) create mode 100644 tests/nextflow.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 947c874..9034d1d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -104,7 +104,7 @@ jobs: - name: Run nf-test run: | - nf-test test --verbose --tag ${{ matrix.tags }} --profile test,"${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap + nf-test test --verbose --tag ${{ matrix.tags }} --profile "${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap - uses: pcolby/tap-summary@v1 with: diff --git a/conf/test_data.config b/conf/test_data.config index 2d4f56c..b522eac 100644 --- a/conf/test_data.config +++ b/conf/test_data.config @@ -2,11 +2,9 @@ // https://github.com/nf-core/test-datasets/blob/modules/README.md params { - // Base directory for test data - nf_core_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules" + // Base directories for test data phageannotator_test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/phageannotator" - modules_testdata_base_path = "s3://ngi-igenomes/testdata/nf-core/modules/" + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' test_data { 'assets' { @@ -47,558 +45,558 @@ params { } 'sarscov2' { 'genome' { - genome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta" - genome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz" - genome_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai" - genome_fasta_txt_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst" - genome_dict = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.dict" - genome_gff3 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gff3" - genome_gff3_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz" - genome_gtf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.gtf" - genome_paf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.paf" - genome_sizes = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/genome.sizes" - transcriptome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta" - transcriptome_paf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf" - proteome_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/proteome.fasta" - proteome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz" + genome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta" + genome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.gz" + genome_fasta_fai = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.fai" + genome_fasta_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.fasta.txt.zst" + genome_dict = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3" + genome_gff3_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gff3.gz" + genome_gtf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.gtf" + genome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.paf" + genome_sizes = "${params.test_data_base}/data/genomics/sarscov2/genome/genome.sizes" + transcriptome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.fasta" + transcriptome_paf = "${params.test_data_base}/data/genomics/sarscov2/genome/transcriptome.paf" + proteome_fasta = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta" + proteome_fasta_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/proteome.fasta.gz" - test_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed" - test_bed_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz" - test2_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed" - test_bed12 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12" - baits_bed = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed" - bed_autosql = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as" + test_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed" + test_bed_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed.gz" + test2_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test2.bed" + test_bed12 = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/test.bed12" + baits_bed = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/baits.bed" + bed_autosql = "${params.test_data_base}/data/genomics/sarscov2/genome/bed/bed6alt.as" - reference_cnn = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn" + reference_cnn = "${params.test_data_base}/data/genomics/sarscov2/genome/cnn/reference.cnn" - kraken2 = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2" - kraken2_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz" + kraken2 = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2" + kraken2_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2.tar.gz" - kraken2_bracken = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken" - kraken2_bracken_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" + kraken2_bracken = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken" + kraken2_bracken_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz" - kaiju = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kaiju" - kaiju_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz" + kaiju = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju" + kaiju_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kaiju.tar.gz" - kofamscan_profiles_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" - kofamscan_ko_list_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" + kofamscan_profiles_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz" + kofamscan_ko_list_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/kofamscan/ko_list.gz" - ncbi_taxmap_zip = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" - taxon_list_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" + ncbi_taxmap_zip = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip" + taxon_list_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/db/maltextract/taxon_list.txt" - mmseqs_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz" + mmseqs_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/mmseqs.tar.gz" - resfinder_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz" + resfinder_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/db/resfinder.tar.gz" - all_sites_fas = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas" - informative_sites_fas = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas" + all_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/all_sites.fas" + informative_sites_fas = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/informative_sites.fas" - contigs_genome_maf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" - contigs_genome_par = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par" - lastdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" + contigs_genome_maf_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz" + contigs_genome_par = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/contigs.genome.par" + lastdb_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/genome/alignment/last/lastdb.tar.gz" - baits_interval_list = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list" - targets_interval_list = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list" - regions_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt" - lc_extrap_mr = "${params.nf_core_test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr" + baits_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/baits.interval_list" + targets_interval_list = "${params.test_data_base}/data/genomics/sarscov2/genome/picard/targets.interval_list" + regions_txt = "${params.test_data_base}/data/genomics/sarscov2/genome/graphtyper/regions.txt" + lc_extrap_mr = "${params.test_data_base}/data/delete_me/preseq/SRR1003759_5M_subset.mr" } 'illumina' { - test_single_end_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam" - test_single_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" - test_single_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" - test_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" - test_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" - test_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" - test_paired_end_methylated_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" - test_paired_end_methylated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" - test_paired_end_methylated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" - test_unaligned_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam" - - test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" - test_interleaved_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" - test_1_fastq_txt_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst" - test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" - test_methylated_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" - test_methylated_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" - test_1_fastq_gz_fastqc_html = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html" - test_1_fastq_gz_fastqc_zip = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" - - test_bedgraph = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph" - - test_bigwig = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig" - - test_wig_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz" - - test_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" - - test_computematrix_mat_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" - - test_bcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf" - - test_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf" - test_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz" - test_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" - test2_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf" - test2_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" - test2_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" - test2_vcf_targets_tsv_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" - test3_vcf = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf" - test3_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz" - test3_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" - - contigs_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta" - scaffolds_fasta = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" - - assembly_gfa = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa" - assembly_gfa_bgz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" - assembly_gfa_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" - assembly_gfa_zst = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" - - test_single_end_bam_readlist_txt = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" - - SRR13255544_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" - SRR11140744_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" + test_single_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.bam" + test_single_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam" + test_single_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai" + test_paired_end_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.bam" + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_methylated_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam" + test_paired_end_methylated_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam" + test_paired_end_methylated_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai" + test_unaligned_bam = "${params.test_data_base}/data/genomics/sarscov2/illumina/bam/test.unaligned.bam" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz" + test_interleaved_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz" + test_1_fastq_txt_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test_1.fastq.txt.zst" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test2_2.fastq.gz" + test_methylated_1_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz" + test_methylated_2_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz" + test_1_fastq_gz_fastqc_html = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.html" + test_1_fastq_gz_fastqc_zip = "${params.test_data_base}/data/genomics/sarscov2/illumina/fastqc/test_fastqc.zip" + + test_bedgraph = "${params.test_data_base}/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph" + + test_bigwig = "${params.test_data_base}/data/genomics/sarscov2/illumina/bigwig/test.bigwig" + + test_wig_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/wig/test.wig.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/sarscov2/illumina/gatk/test.baserecalibrator.table" + + test_computematrix_mat_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz" + + test_bcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.bcf" + + test_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf" + test_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz" + test_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi" + test2_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf" + test2_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz" + test2_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi" + test2_vcf_targets_tsv_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz" + test3_vcf = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf" + test3_vcf_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz" + test3_vcf_gz_tbi = "${params.test_data_base}/data/genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi" + + contigs_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/contigs.fasta" + scaffolds_fasta = "${params.test_data_base}/data/genomics/sarscov2/illumina/fasta/scaffolds.fasta" + + assembly_gfa = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa" + assembly_gfa_bgz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz" + assembly_gfa_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.gz" + assembly_gfa_zst = "${params.test_data_base}/data/genomics/sarscov2/illumina/gfa/assembly.gfa.zst" + + test_single_end_bam_readlist_txt = "${params.test_data_base}/data/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt" + + SRR13255544_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR13255544.tar.gz" + SRR11140744_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/illumina/sra/SRR11140744.tar.gz" } 'nanopore' { - test_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam" - test_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" + test_sorted_bam = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam" + test_sorted_bam_bai = "${params.test_data_base}/data/genomics/sarscov2/nanopore/bam/test.sorted.bam.bai" - fast5_tar_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" + fast5_tar_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fast5/fast5.tar.gz" - test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz" + test_fastq_gz = "${params.test_data_base}/data/genomics/sarscov2/nanopore/fastq/test.fastq.gz" - test_sequencing_summary = "${params.nf_core_test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" + test_sequencing_summary = "${params.test_data_base}/data/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt" } 'metagenome' { - classified_reads_assignment = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" - kraken_report = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" - krona_taxonomy = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab" - seqid2taxid_map = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map" - nodes_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp" - names_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/names.dmp" - prot_nodes_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp" - prot_names_dmp = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp" - prot_accession2taxid_gz = "${params.nf_core_test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz" + classified_reads_assignment = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.reads.txt" + kraken_report = "${params.test_data_base}/data/genomics/sarscov2/metagenome/test_1.kraken2.report.txt" + krona_taxonomy = "${params.test_data_base}/data/genomics/sarscov2/metagenome/krona_taxonomy.tab" + seqid2taxid_map = "${params.test_data_base}/data/genomics/sarscov2/metagenome/seqid2taxid.map" + nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/nodes.dmp" + names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/names.dmp" + prot_nodes_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_nodes.dmp" + prot_names_dmp = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot_names.dmp" + prot_accession2taxid_gz = "${params.test_data_base}/data/genomics/sarscov2/metagenome/prot.accession2taxid.gz" } } 'mus_musculus' { 'genome' { - rnaseq_samplesheet = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" - rnaseq_genemeta = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" - rnaseq_contrasts = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" - rnaseq_matrix = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" - rnaseq_lengths = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv" - deseq_results = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" - genome_19_fasta = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz" - genome_19_gtf = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz" + rnaseq_samplesheet = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.samplesheet.csv" + rnaseq_genemeta = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.gene_meta.tsv" + rnaseq_contrasts = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.contrasts.csv" + rnaseq_matrix = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.gene_counts.top1000cov.tsv" + rnaseq_lengths = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.spoofed_lengths.tsv" + deseq_results = "${params.test_data_base}/data/genomics/mus_musculus/rnaseq_expression/SRP254919.salmon.merged.deseq2.results.tsv" + genome_19_fasta = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.fa.gz" + genome_19_gtf = "${params.test_data_base}/data/genomics/mus_musculus/genome/chr19.filtered.gtf.gz" } 'illumina' { - test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" - test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" - genome_config = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json" - multiome_lib_csv = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv" - test_scARC_gex_R1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz" - test_scARC_gex_R2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz" - test_scARC_atac_R1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz" - test_scARC_atac_R2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz" - test_scARC_atac_I2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz" + test_1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376998.small.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/mageck/ERR376999.small.fastq.gz" + genome_config = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json" + multiome_lib_csv = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/lib.csv" + test_scARC_gex_R1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_gex_R2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_R1_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz" + test_scARC_atac_R2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz" + test_scARC_atac_I2_fastq_gz = "${params.test_data_base}/data/genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz" } 'csv' { - count_table = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv" - library = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv" + count_table = "${params.test_data_base}/data/genomics/mus_musculus/mageck/count_table.csv" + library = "${params.test_data_base}/data/genomics/mus_musculus/mageck/yusa_library.csv" } 'txt' { - design_matrix = "${params.nf_core_test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt" + design_matrix = "${params.test_data_base}/data/genomics/mus_musculus/mageck/design_matrix.txt" } } 'homo_sapiens' { '10xgenomics' { cellranger { - test_10x_10k_pbmc_5fb_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_5fb_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_5gex_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_5gex_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_b_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_b_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_t_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_t_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv" - - test_10x_10k_pbmc_cmo_cmo_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_cmo_cmo_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_cmo_gex1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_cmo_gex1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_cmo_gex2_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz" - test_10x_10k_pbmc_cmo_gex2_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz" - test_10x_10k_pbmc_cmo_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv" - - test_10x_5k_cmvpos_tcells_ab_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz" - test_10x_5k_cmvpos_tcells_ab_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz" - test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz" - test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz" - test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz" - test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz" - test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" - - test_10x_vdj_ref_json = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json" - test_10x_vdj_ref_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa" - test_10x_vdj_ref_suppfasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa" - - test_scATAC_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz" - test_scATAC_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz" - test_scATAC_3_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz" - test_scATAC_I_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz" + test_10x_10k_pbmc_5fb_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5fb_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5fb/subsampled_sc5p_v2_hs_PBMC_10k_5fb_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_5gex_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/5gex/5gex/subsampled_sc5p_v2_hs_PBMC_10k_5gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_b_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/bcell/subsampled_sc5p_v2_hs_PBMC_10k_b_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_t_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/fastqs/tcell/subsampled_sc5p_v2_hs_PBMC_10k_t_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc/sc5p_v2_hs_PBMC_10k_multi_5gex_5fb_b_t_feature_ref.csv" + + test_10x_10k_pbmc_cmo_cmo_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_cmo_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/cmo/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_multiplexing_capture_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_1/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R1_001.fastq.gz" + test_10x_10k_pbmc_cmo_gex2_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/fastqs/gex_2/subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_2_gex_S1_L001_R2_001.fastq.gz" + test_10x_10k_pbmc_cmo_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/10k_pbmc_cmo/10k_pbmc_cmo_count_feature_reference.csv" + + test_10x_5k_cmvpos_tcells_ab_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_ab_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/ab/subsampled_5k_human_antiCMV_T_TBNK_connect_AB_S2_L004_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_gex1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/gex_1/subsampled_5k_human_antiCMV_T_TBNK_connect_GEX_1_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R1_001.fastq.gz" + test_10x_5k_cmvpos_tcells_vdj_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/fastqs/vdj/subsampled_5k_human_antiCMV_T_TBNK_connect_VDJ_S1_L001_R2_001.fastq.gz" + test_10x_5k_cmvpos_tcells_feature_ref_csv = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/5k_cmvpos_tcells/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" + + test_10x_vdj_ref_json = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/reference.json" + test_10x_vdj_ref_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/regions.fa" + test_10x_vdj_ref_suppfasta = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger/references/vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0/fasta/supp_regions.fa" + + test_scATAC_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R1_001.fastq.gz" + test_scATAC_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R2_001.fastq.gz" + test_scATAC_3_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_R3_001.fastq.gz" + test_scATAC_I_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/cellranger-atac/test_scATAC_S1_L001_I1_001.fastq.gz" } spaceranger { - test_10x_ffpe_cytassist_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz" - test_10x_ffpe_cytassist_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz" - test_10x_ffpe_cytassist_image = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif" - test_10x_ffpe_cytassist_probeset = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv" - - test_10x_ffpe_v1_fastq_1_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz" - test_10x_ffpe_v1_fastq_2_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz" - test_10x_ffpe_v1_image = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" + test_10x_ffpe_cytassist_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_cytassist_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_cytassist_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif" + test_10x_ffpe_cytassist_probeset = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv" + + test_10x_ffpe_v1_fastq_1_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz" + test_10x_ffpe_v1_fastq_2_gz = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz" + test_10x_ffpe_v1_image = "${params.test_data_base}/data/genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" } } 'genome' { - genome_elfasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta" - genome_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta" - genome_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" - genome_fasta_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz" - genome_fasta_gz_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai" - genome_fasta_gz_gzi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi" - genome_strtablefile = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip" - genome_dict = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.dict" - genome_gff3 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3" - genome_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf" - genome_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list" - genome_multi_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed" - genome_blacklist_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed" - genome_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes" - genome_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed" - genome_header = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.header" - genome_bed_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz" - genome_bed_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi" - genome_elsites = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites" - transcriptome_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta" - genome2_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta" - genome_chain_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz" - genome_annotated_interval_tsv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv" - genome_mt_gb = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb" - genome_preprocessed_count_tsv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv" - genome_preprocessed_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list" - genome_ploidy_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz" - genome_ploidy_calls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz" - genome_germline_cnv_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz" - genome_germline_cnv_calls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz" - genome_motifs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt" - genome_config = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json" - - genome_1_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz" - genome_1_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf" - - genome_21_sdf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" - genome_21_fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" - genome_21_fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" - genome_21_gencode_gtf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf" - genome_21_dict = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" - genome_21_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" - genome_21_interval_list = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" - genome_21_annotated_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed" - genome_21_multi_interval_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" - genome_21_multi_interval_antitarget_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" - genome_21_multi_interval_bed_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" - genome_21_multi_interval_bed_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" - genome_21_chromosomes_dir = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" - genome_21_reference_cnn = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" - genome_21_eigenstrat_snp = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp" - genome_21_stitch_posfile = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv" - - dbsnp_146_hg38_elsites = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" - dbsnp_146_hg38_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" - dbsnp_146_hg38_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" - gnomad_r2_1_1_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" - gnomad_r2_1_1_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" - mills_and_1000g_indels_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" - mills_and_1000g_indels_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" - syntheticvcf_short_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" - syntheticvcf_short_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" - syntheticvcf_short_score = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" - gnomad_r2_1_1_sv_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" - gnomad2_r2_1_1_sv_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" - - hapmap_3_3_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" - hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" - res_1000g_omni2_5_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" - res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" - res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" - res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" - dbsnp_138_hg38_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" - dbsnp_138_hg38_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" - gnomad_r2_1_1_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" - gnomad_r2_1_1_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" - mills_and_1000g_indels_21_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" - mills_and_1000g_indels_21_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" - haplotype_map = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" - dbNSFP_4_1a_21_hg38_txt_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz" - dbNSFP_4_1a_21_hg38_txt_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi" - ngscheckmate_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" - - index_salmon = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/index/salmon" - repeat_expansions = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json" - justhusky_ped = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" - justhusky_minimal_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" - justhusky_minimal_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" - - vcfanno_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" - vcfanno_toml = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" - updsites_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed" - - prg_input = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip" - crispr_functional_counts = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv" - crispr_functional_library = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv" - - vep_cache = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz" - affy_array_samplesheet = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv" - affy_array_celfiles_tar = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar" + genome_elfasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elfasta" + genome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta" + genome_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.fai" + genome_fasta_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz" + genome_fasta_gz_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.fai" + genome_fasta_gz_gzi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.fasta.gz.gzi" + genome_strtablefile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_strtablefile.zip" + genome_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.dict" + genome_gff3 = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gff3" + genome_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.gtf" + genome_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.interval_list" + genome_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.multi_intervals.bed" + genome_blacklist_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed" + genome_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.sizes" + genome_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed" + genome_header = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.header" + genome_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz" + genome_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.bed.gz.tbi" + genome_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.elsites" + transcriptome_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/transcriptome.fasta" + genome2_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome2.fasta" + genome_chain_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.chain.gz" + genome_annotated_interval_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.annotated_intervals.tsv" + genome_mt_gb = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.NC_012920_1.gb" + genome_preprocessed_count_tsv = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.counts.tsv" + genome_preprocessed_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.preprocessed_intervals.interval_list" + genome_ploidy_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_model.tar.gz" + genome_ploidy_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.ploidy_calls.tar.gz" + genome_germline_cnv_model = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_model.tar.gz" + genome_germline_cnv_calls = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome.germline_cnv_calls.tar.gz" + genome_motifs = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_motifs.txt" + genome_config = "${params.test_data_base}/data/genomics/homo_sapiens/genome/genome_config.json" + + genome_1_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.fasta.gz" + genome_1_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr1/genome.gtf" + + genome_21_sdf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz" + genome_21_fasta = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + genome_21_fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" + genome_21_gencode_gtf = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr21_gencode.gtf" + genome_21_dict = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" + genome_21_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.sizes" + genome_21_interval_list = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_annotated_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/annotated.bed" + genome_21_multi_interval_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_antitarget_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.antitarget.bed" + genome_21_multi_interval_bed_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" + genome_21_chromosomes_dir = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz" + genome_21_reference_cnn = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn" + genome_21_eigenstrat_snp = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/chr_21.snp" + genome_21_stitch_posfile = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/sequence/dbsnp_138.hg38.first_10_biallelic_sites.tsv" + + dbsnp_146_hg38_elsites = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites" + dbsnp_146_hg38_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_146_hg38_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + gnomad_r2_1_1_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + mills_and_1000g_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + syntheticvcf_short_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz" + syntheticvcf_short_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi" + syntheticvcf_short_score = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score" + gnomad_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz" + gnomad2_r2_1_1_sv_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz" + + hapmap_3_3_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz" + hapmap_3_3_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi" + res_1000g_omni2_5_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz" + res_1000g_omni2_5_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_omni2.5.hg38.vcf.gz.tbi" + res_1000g_phase1_snps_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz" + res_1000g_phase1_snps_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/1000G_phase1.snps.hg38.vcf.gz.tbi" + dbsnp_138_hg38_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz" + dbsnp_138_hg38_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi" + gnomad_r2_1_1_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz" + gnomad_r2_1_1_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi" + mills_and_1000g_indels_21_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz" + mills_and_1000g_indels_21_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi" + haplotype_map = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt" + dbNSFP_4_1a_21_hg38_txt_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz" + dbNSFP_4_1a_21_hg38_txt_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/dbNSFP4.1a.21.txt.gz.tbi" + ngscheckmate_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/chr21/germlineresources/SNP_GRCh38_hg38_wChr.bed" + + index_salmon = "${params.test_data_base}/data/genomics/homo_sapiens/genome/index/salmon" + repeat_expansions = "${params.test_data_base}/data/genomics/homo_sapiens/genome/loci/repeat_expansions.json" + justhusky_ped = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped" + justhusky_minimal_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz" + justhusky_minimal_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi" + + vcfanno_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz" + vcfanno_toml = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml" + updsites_bed = "${params.test_data_base}/data/genomics/homo_sapiens/genome/updsites.bed" + + prg_input = "${params.test_data_base}/data/genomics/homo_sapiens/genome/PRG_test.zip" + crispr_functional_counts = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/functional_genomics_counts.tsv" + crispr_functional_library = "${params.test_data_base}/data/genomics/homo_sapiens/genome/tsv/library_functional_genomics.tsv" + + vep_cache = "${params.test_data_base}/data/genomics/homo_sapiens/genome/vep.tar.gz" + affy_array_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751.csv" + affy_array_celfiles_tar = "${params.test_data_base}/data/genomics/homo_sapiens/array_expression/GSE38751_RAW.tar" } 'pangenome' { - pangenome_fa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa" - pangenome_fa_bgzip = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz" - pangenome_fa_bgzip_fai = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai" - pangenome_fa_bgzip_gzi = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" - pangenome_paf = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf" - pangenome_paf_gz = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz" - pangenome_panacus_tsv = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv" - pangenome_seqwish_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa" - pangenome_smoothxg_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" - pangenome_gfaffix_gfa = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" + pangenome_fa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa" + pangenome_fa_bgzip = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz" + pangenome_fa_bgzip_fai = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.fai" + pangenome_fa_bgzip_gzi = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.fa.gz.gzi" + pangenome_paf = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf" + pangenome_paf_gz = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.paf.gz" + pangenome_panacus_tsv = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.panacus.tsv" + pangenome_seqwish_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.seqwish.gfa" + pangenome_smoothxg_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.smoothxg.gfa" + pangenome_gfaffix_gfa = "${params.test_data_base}/data/pangenomics/homo_sapiens/pangenome.gfaffix.gfa" 'odgi' { - pangenome_og = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og" - pangenome_lay = "${params.nf_core_test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay" + pangenome_og = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.og" + pangenome_lay = "${params.test_data_base}/data/pangenomics/homo_sapiens/odgi/pangenome.lay" } } 'illumina' { - test_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" - test_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" - test_paired_end_name_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" - test_paired_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" - test_paired_end_markduplicates_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" - test_paired_end_markduplicates_sorted_referencesn_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" - test_paired_end_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" - test_paired_end_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" - test_paired_end_umi_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" - test_paired_end_umi_converted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" - test_paired_end_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" - test_paired_end_umi_histogram_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" - test_paired_end_umi_unsorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" - test_paired_end_umi_unsorted_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" - test_paired_end_hla = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" - test_paired_end_hla_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" - test_paired_end_hla_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" - test_rna_paired_end_sorted_chr6_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam" - test_rna_paired_end_sorted_chr6_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai" - - test2_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" - test2_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" - test2_paired_end_name_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" - test2_paired_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" - test2_paired_end_markduplicates_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" - test2_paired_end_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" - test2_paired_end_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" - test2_paired_end_umi_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" - test2_paired_end_umi_converted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" - test2_paired_end_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" - test2_paired_end_umi_histogram_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" - test2_paired_end_umi_unsorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" - test2_paired_end_umi_unsorted_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" - test_paired_end_duplex_umi_unmapped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" - test_paired_end_duplex_umi_mapped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" - test_paired_end_duplex_umi_mapped_tagged_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" - test_paired_end_duplex_umi_grouped_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" - test_paired_end_duplex_umi_duplex_consensus_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" - - mitochon_standin_recalibrated_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" - mitochon_standin_recalibrated_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" - test_illumina_mt_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam" - test_illumina_mt_bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai" - - test3_single_end_markduplicates_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" - - read_group_settings_txt = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" - - test_paired_end_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" - test_paired_end_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" - test_paired_end_markduplicates_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" - test_paired_end_markduplicates_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" - test_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" - test_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" - - test2_paired_end_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" - test2_paired_end_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" - test2_paired_end_markduplicates_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" - test2_paired_end_markduplicates_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" - test2_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" - test2_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" - test3_paired_end_recalibrated_sorted_cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram" - test3_paired_end_recalibrated_sorted_cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai" - - test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" - test_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" - test_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" - test_airrseq_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz" - test_airrseq_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz" - test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" - test2_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" - test2_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" - test_rnaseq_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" - test_rnaseq_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" - test_paired_end_duplex_umi_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" - test_paired_end_duplex_umi_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" - - test_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" - test2_baserecalibrator_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" - test_pileups_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table" - test2_pileups_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" - - test_paired_end_sorted_dragstrmodel = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" - - test_genomicsdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" - test_pon_genomicsdb_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" - - test2_haplotc_ann_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" - test2_haplotc_ann_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" - test_haplotc_cnn_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" - test_haplotc_cnn_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" - - test2_haplotc_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" - test2_haplotc_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" - - test2_recal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" - test2_recal_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" - test2_tranches = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" - test2_allele_specific_recal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" - test2_allele_specific_recal_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" - test2_allele_specific_tranches = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" - - test_test2_paired_mutect2_calls_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" - test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" - test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" - test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" - test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" - test_test2_paired_segmentation_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" - test_test2_paired_contamination_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" - - test_genome_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" - test_genome_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" - test_genome_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" - test_genome_vcf_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" - - test_genome_vcf_ud = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" - test_genome_vcf_mu = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" - test_genome_vcf_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" - - test2_genome_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" - test2_genome_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" - test2_genome_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" - test2_genome_vcf_idx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" - - test_genome21_indels_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" - test_genome21_indels_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" - - test_mpileup = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" - test2_mpileup = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" - - test_broadpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" - test2_broadpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" - - test_narrowpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" - test2_narrowpeak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" - - test_yak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak" - test2_yak = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak" - - cutandrun_bedgraph_test_1 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" - cutandrun_bedgraph_test_2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" - na24385_chr22_coverage = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed" - - empty_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz" - empty_vcf_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi" - - simulated_sv = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz" - simulated_sv_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi" - simulated_sv2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz" - simulated_sv2_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi" - - test_rnaseq_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" - test_sv_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" - test_sv_vcf_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi" - na24385_chr22_sv_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz" - na24385_chr22_sv_vcf_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi" - genmod_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" - genmod_annotate_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" - genmod_models_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" - genmod_score_vcf_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" - - test_mito_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" - - test_pytor = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor" - rank_model = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" - - test_flowcell = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" - test_flowcell_samplesheet = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" - - varlociraptor_scenario = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml" - - contig_ploidy_priors_table = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" - - purecn_ex1_bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam" - purecn_ex1_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai" - purecn_ex1_interval = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt" - purecn_ex1_normal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz" - purecn_ex2_normal = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz" - purecn_normalpanel_vcf = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz" - purecn_normalpanel_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi" + test_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam" + test_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai" + test_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.name.sorted.bam" + test_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam" + test_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai" + test_paired_end_markduplicates_sorted_referencesn_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.referencesn.txt" + test_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam" + test_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai" + test_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_consensus.bam" + test_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_converted.bam" + test_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_grouped.bam" + test_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_histogram.txt" + test_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.umi_unsorted.bam" + test_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.unsorted_tagged.bam" + test_paired_end_hla = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam" + test_paired_end_hla_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam" + test_paired_end_hla_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai" + test_rna_paired_end_sorted_chr6_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam" + test_rna_paired_end_sorted_chr6_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai" + + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai" + test2_paired_end_name_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam" + test2_paired_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam" + test2_paired_end_markduplicates_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai" + test2_paired_end_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam" + test2_paired_end_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai" + test2_paired_end_umi_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam" + test2_paired_end_umi_converted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam" + test2_paired_end_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam" + test2_paired_end_umi_histogram_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt" + test2_paired_end_umi_unsorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam" + test2_paired_end_umi_unsorted_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam" + test_paired_end_duplex_umi_unmapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_unmapped.bam" + test_paired_end_duplex_umi_mapped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped.bam" + test_paired_end_duplex_umi_mapped_tagged_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_mapped_tagged.bam" + test_paired_end_duplex_umi_grouped_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_grouped.bam" + test_paired_end_duplex_umi_duplex_consensus_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/umi/test.paired_end.duplex_umi_duplex_consensus.bam" + + mitochon_standin_recalibrated_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam" + mitochon_standin_recalibrated_sorted_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai" + test_illumina_mt_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam" + test_illumina_mt_bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai" + + test3_single_end_markduplicates_sorted_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam" + + read_group_settings_txt = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bam/read_group_settings.txt" + + test_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram" + test_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai" + test_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram" + test_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai" + test_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram" + test_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai" + + test2_paired_end_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram" + test2_paired_end_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai" + test2_paired_end_markduplicates_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram" + test2_paired_end_markduplicates_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai" + test2_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram" + test2_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai" + test3_paired_end_recalibrated_sorted_cram = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram" + test3_paired_end_recalibrated_sorted_cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/cram/test3.paired_end.recalibrated.sorted.cram.crai" + + test_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz" + test_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz" + test_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz" + test_airrseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_umi_R1.fastq.gz" + test_airrseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_airrseq_R2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz" + test2_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz" + test2_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz" + test_rnaseq_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz" + test_rnaseq_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz" + test_paired_end_duplex_umi_1_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_1.fastq.gz" + test_paired_end_duplex_umi_2_fastq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/fastq/test_duplex_umi_2.fastq.gz" + + test_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table" + test2_baserecalibrator_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table" + test_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test.pileups.table" + test2_pileups_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test2.pileups.table" + + test_paired_end_sorted_dragstrmodel = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt" + + test_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz" + test_pon_genomicsdb_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz" + + test2_haplotc_ann_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz" + test2_haplotc_ann_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi" + test_haplotc_cnn_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz" + test_haplotc_cnn_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi" + + test2_haplotc_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz" + test2_haplotc_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi" + + test2_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal" + test2_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx" + test2_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches" + test2_allele_specific_recal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal" + test2_allele_specific_recal_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx" + test2_allele_specific_tranches = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches" + + test_test2_paired_mutect2_calls_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz" + test_test2_paired_mutect2_calls_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi" + test_test2_paired_mutect2_calls_vcf_gz_stats = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats" + test_test2_paired_mutect2_calls_f1r2_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz" + test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz" + test_test2_paired_segmentation_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table" + test_test2_paired_contamination_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table" + + test_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf" + test_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz" + test_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi" + test_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx" + + test_genome_vcf_ud = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.UD" + test_genome_vcf_mu = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.mu" + test_genome_vcf_bed = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/svd/test.genome.vcf.bed" + + test2_genome_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf" + test2_genome_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz" + test2_genome_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" + test2_genome_vcf_idx = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + + test_genome21_indels_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + + test_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz" + test2_mpileup = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz" + + test_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" + test2_broadpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" + + test_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak" + test2_narrowpeak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak" + + test_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test.yak" + test2_yak = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/yak/test2.yak" + + cutandrun_bedgraph_test_1 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph" + cutandrun_bedgraph_test_2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph" + na24385_chr22_coverage = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bedgraph/NA24385_coverage.bed" + + empty_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz" + empty_vcf_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/empty.vcf.gz.tbi" + + simulated_sv = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz" + simulated_sv_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv.vcf.gz.tbi" + simulated_sv2 = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz" + simulated_sv2_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/chr21/simulated_sv2.vcf.gz.tbi" + + test_rnaseq_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf" + test_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz" + test_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz.tbi" + na24385_chr22_sv_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz" + na24385_chr22_sv_vcf_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi" + genmod_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/genmod.vcf.gz" + genmod_annotate_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_annotate.vcf.gz" + genmod_models_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_models.vcf.gz" + genmod_score_vcf_gz = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/test_score.vcf.gz" + + test_mito_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz" + + test_pytor = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/pytor/test.pytor" + rank_model = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/genmod/svrank_model_-v1.8-.ini" + + test_flowcell = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz" + test_flowcell_samplesheet = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/bcl/flowcell_samplesheet.csv" + + varlociraptor_scenario = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/varlociraptor/scenario.yml" + + contig_ploidy_priors_table = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/gatk/contig_ploidy_priors_table.tsv" + + purecn_ex1_bam = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam" + purecn_ex1_bai = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1.bam.bai" + purecn_ex1_interval = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_intervals.txt" + purecn_ex1_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex1_normal.txt.gz" + purecn_ex2_normal = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_ex2_normal.txt.gz" + purecn_normalpanel_vcf = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz" + purecn_normalpanel_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/illumina/purecn/purecn_normalpanel.vcf.gz.tbi" } 'pacbio' { - primers = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta" - alz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam" - alzpbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" - ccs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" - ccs_fa = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" - ccs_fa_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" - ccs_fq = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" - ccs_fq_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" - ccs_xml = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" - hifi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" - lima = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" - refine = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" - cluster = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" - singletons = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" - aligned = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" - alignedbai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" - genemodel1 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" - genemodel2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" - filelist = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt" + primers = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/primers.fasta" + alz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam" + alzpbi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi" + ccs = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam" + ccs_fa = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta" + ccs_fa_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz" + ccs_fq = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq" + ccs_fq_gz = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz" + ccs_xml = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml" + hifi = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz" + lima = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam" + refine = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam" + cluster = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam" + singletons = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam" + aligned = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam" + alignedbai = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai" + genemodel1 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed" + genemodel2 = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed" + filelist = "${params.test_data_base}/data/genomics/homo_sapiens/pacbio/txt/filelist.txt" } 'scramble' { - fasta = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.fa" - fasta_fai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai" - bam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bam" - bam_bai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai" - cram = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.cram" - cram_crai = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai" - bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/scramble/test.bed" + fasta = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa" + fasta_fai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.fa.fai" + bam = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam" + bam_bai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bam.bai" + cram = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram" + cram_crai = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.cram.crai" + bed = "${params.test_data_base}/data/genomics/homo_sapiens/scramble/test.bed" } 'gene_set_analysis' { - gct = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct" - cls = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls" - gmx = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx" + gct = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples_collapsed_symbols.gct" + cls = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/P53_6samples.cls" + gmx = "${params.test_data_base}/data/genomics/homo_sapiens/gene_set_analysis/c1.symbols.reduced.gmx" } 'cnvkit' { amplicon_cnr = "https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cnr" @@ -607,205 +605,205 @@ params { } 'bacteroides_fragilis' { 'genome' { - genome_fna_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" - genome_gbff_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" - genome_paf = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" - genome_gff_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + genome_gbff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz" + genome_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf" + genome_gff_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gff.gz" } 'hamronization' { - genome_abricate_tsv = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" - genome_mapping_potential_arg = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" + genome_abricate_tsv = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv" + genome_mapping_potential_arg = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.mapping.potential.ARG" } 'illumina' { - test1_contigs_fa_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" - test1_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" - test1_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" - test2_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" - test2_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" - test1_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" - test1_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" - test1_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" - test2_paired_end_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" - test2_paired_end_sorted_bam = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" - test2_paired_end_sorted_bam_bai = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" + test1_contigs_fa_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz" + test1_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz" + test1_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz" + test2_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz" + test2_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz" + test1_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam" + test1_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam" + test1_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai" + test2_paired_end_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam" + test2_paired_end_sorted_bam = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam" + test2_paired_end_sorted_bam_bai = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai" } 'nanopore' { - test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" - overlap_paf = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz" + overlap_paf = "${params.test_data_base}/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf" } } 'candidatus_portiera_aleyrodidarum' { 'genome' { - //genome_fasta = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" - genome_sizes = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" - genome_aln_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" - genome_aln_nwk = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" - proteome_fasta = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" - test1_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" - test2_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" - test3_gff = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" + //genome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta" + genome_sizes = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk" + proteome_fasta = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta" + test1_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff" + test2_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff" + test3_gff = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff" } 'illumina' { - test_1_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" - test_2_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" - test_se_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" + test_1_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_1.fastq.gz" + test_2_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz" + test_se_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz" } 'nanopore' { - test_fastq_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" + test_fastq_gz = "${params.test_data_base}/data/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz" } } 'haemophilus_influenzae' { 'genome' { - genome_fna_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" - genome_aln_gz = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" - genome_aln_nwk = "${params.nf_core_test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" + genome_fna_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz" + genome_aln_gz = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz" + genome_aln_nwk = "${params.test_data_base}/data/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk" } } 'generic' { 'csv' { - test_csv = "${params.nf_core_test_data_base}/data/generic/csv/test.csv" + test_csv = "${params.test_data_base}/data/generic/csv/test.csv" } 'notebooks' { - rmarkdown = "${params.nf_core_test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" - ipython_md = "${params.nf_core_test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md" - ipython_ipynb = "${params.nf_core_test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb" + rmarkdown = "${params.test_data_base}/data/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd" + ipython_md = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.md" + ipython_ipynb = "${params.test_data_base}/data/generic/notebooks/jupyter/ipython_notebook.ipynb" } 'tar' { - tar_gz = "${params.nf_core_test_data_base}/data/generic/tar/hello.tar.gz" + tar_gz = "${params.test_data_base}/data/generic/tar/hello.tar.gz" } 'tsv' { - test_tsv = "${params.nf_core_test_data_base}/data/generic/tsv/test.tsv" + test_tsv = "${params.test_data_base}/data/generic/tsv/test.tsv" } 'txt' { - hello = "${params.nf_core_test_data_base}/data/generic/txt/hello.txt" + hello = "${params.test_data_base}/data/generic/txt/hello.txt" } 'cooler'{ - test_pairix_pair_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" - test_pairix_pair_gz_px2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" - test_pairs_pair = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" - test_tabix_pair_gz = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" - test_tabix_pair_gz_tbi = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" - hg19_chrom_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" - test_merge_cool = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" - test_merge_cool_cp2 = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" + test_pairix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz" + test_pairix_pair_gz_px2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2" + test_pairs_pair = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs" + test_tabix_pair_gz = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz" + test_tabix_pair_gz_tbi = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi" + hg19_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes" + test_merge_cool = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool" + test_merge_cool_cp2 = "${params.test_data_base}/data/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool" } 'pairtools' { - mock_4dedup_pairsam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam" - mock_4flip_pairs = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs" - mock_chrom_sizes = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes" - mock_pairsam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam" - mock_sam = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam" - frag_bed = "${params.nf_core_test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed" + mock_4dedup_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4dedup.pairsam" + mock_4flip_pairs = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.4flip.pairs" + mock_chrom_sizes = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.chrom.sizes" + mock_pairsam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.pairsam" + mock_sam = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/mock.sam" + frag_bed = "${params.test_data_base}/data/genomics/homo_sapiens/pairtools/frag.bed" } 'estsfs'{ - config_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/config-JC.txt" - data_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT" - seed_file = "${params.nf_core_test_data_base}/data/delete_me/estsfs/seedfile.txt" + config_file = "${params.test_data_base}/data/delete_me/estsfs/config-JC.txt" + data_file = "${params.test_data_base}/data/delete_me/estsfs/TEST-DATA.TXT" + seed_file = "${params.test_data_base}/data/delete_me/estsfs/seedfile.txt" } 'config' { - ncbi_user_settings = "${params.nf_core_test_data_base}/data/generic/config/ncbi_user_settings.mkfg" + ncbi_user_settings = "${params.test_data_base}/data/generic/config/ncbi_user_settings.mkfg" } 'unsorted_data' { 'unsorted_text' { - genome_file = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome" - intervals = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed" - numbers_csv = "${params.nf_core_test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv" + genome_file = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.genome" + intervals = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.bed" + numbers_csv = "${params.test_data_base}/data/generic/unsorted_data/unsorted_text/test.csv" } } } 'proteomics' { 'msspectra' { - ups_file1 = "${params.nf_core_test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw" - ups_file2 = "${params.nf_core_test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw" - profile_spectra = "${params.nf_core_test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML" - hla2_file = "${params.nf_core_test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw" + ups_file1 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_12.raw" + ups_file2 = "${params.test_data_base}/data/proteomics/msspectra/OVEMB150205_14.raw" + profile_spectra = "${params.test_data_base}/data/proteomics/msspectra/peakpicker_tutorial_1.mzML" + hla2_file = "${params.test_data_base}/data/proteomics/msspectra/PXD012083_e005640_II.raw" } 'database' { - yeast_ups = "${params.nf_core_test_data_base}/data/proteomics/database/yeast_UPS.fasta" + yeast_ups = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta" } 'maxquant' { - mq_contrasts = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" - mq_proteingroups = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt" - mq_samplesheet = "${params.nf_core_test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv" - mq_proteus_mat = "${params.nf_core_test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv" + mq_contrasts = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" + mq_proteingroups = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_proteinGroups.txt" + mq_samplesheet = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_samplesheet.tsv" + mq_proteus_mat = "${params.test_data_base}/data/proteomics/maxquant/proteus.raw_MaxQuant_proteingroups_tab.tsv" } 'parameter' { - maxquant = "${params.nf_core_test_data_base}/data/proteomics/parameter/mqpar.xml" + maxquant = "${params.test_data_base}/data/proteomics/parameter/mqpar.xml" } 'openms' { - idxml1 = "${params.nf_core_test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML" - idxml2 = "${params.nf_core_test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML" + idxml1 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep1_small.idXML" + idxml2 = "${params.test_data_base}/data/proteomics/openms/HepG2_rep2_small.idXML" } 'pdb' { - tim1_pdb = "${params.nf_core_test_data_base}/data/proteomics/pdb/1tim.pdb" - tim8_pdb = "${params.nf_core_test_data_base}/data/proteomics/pdb/8tim.pdb" + tim1_pdb = "${params.test_data_base}/data/proteomics/pdb/1tim.pdb" + tim8_pdb = "${params.test_data_base}/data/proteomics/pdb/8tim.pdb" } } 'galaxea_fascicularis' { hic { - pretext = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext" + pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext" } } 'deilephila_porcellus' { 'mito' { - ref_fa = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta" - ref_gb = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb" - hifi_reads = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa" - contigs = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa" + ref_fa = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta" + ref_gb = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb" + hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa" + contigs = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa" } } 'arabidopsis_thaliana' { 'plastid' { - hifi_reads = "${params.nf_core_test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta" + hifi_reads = "${params.test_data_base}/data/genomics/eukaryotes/arabidopsis_thaliana/plastid/ddAraThal4.HiFi.reads.fasta" } } 'imaging' { 'h5' { - plant_wga = "${params.nf_core_test_data_base}/data/imaging/h5/plant_wga.h5" - plant_wga_prob = "${params.nf_core_test_data_base}/data/imaging/h5/plant_wga_probabilities.h5" + plant_wga = "${params.test_data_base}/data/imaging/h5/plant_wga.h5" + plant_wga_prob = "${params.test_data_base}/data/imaging/h5/plant_wga_probabilities.h5" } 'ilp' { - plant_wga_multicut = "${params.nf_core_test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp" - plant_wga_pixel_class = "${params.nf_core_test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp" + plant_wga_multicut = "${params.test_data_base}/data/imaging/ilp/plant_wga.multicut.ilp" + plant_wga_pixel_class = "${params.test_data_base}/data/imaging/ilp/plant_wga.pixel_prob.ilp" } 'tiff' { - mouse_heart_wga = "${params.nf_core_test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff" + mouse_heart_wga = "${params.test_data_base}/data/imaging/tiff/mindagap.mouse_heart.wga.tiff" } 'ome-tiff' { - cycif_tonsil_channels = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv" - cycif_tonsil_cycle1 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" - cycif_tonsil_cycle2 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" - cycif_tonsil_cycle3 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif" - cycif_tonsil_dfp = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif" - cycif_tonsil_ffp = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif" + cycif_tonsil_channels = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-channels.csv" + cycif_tonsil_cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycif_tonsil_cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + cycif_tonsil_cycle3 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif" + cycif_tonsil_dfp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-dfp.ome.tif" + cycif_tonsil_ffp = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-ffp.ome.tif" } 'registration' { - markers = "${params.nf_core_test_data_base}/data/imaging/registration/markers.csv" - cycle1 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" - cycle2 = "${params.nf_core_test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" + markers = "${params.test_data_base}/data/imaging/registration/markers.csv" + cycle1 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif" + cycle2 = "${params.test_data_base}/data/imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif" } 'segmentation' { - markers = "${params.nf_core_test_data_base}/data/imaging/segmentation/markers.csv" - image = "${params.nf_core_test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif" + markers = "${params.test_data_base}/data/imaging/segmentation/markers.csv" + image = "${params.test_data_base}/data/imaging/segmentation/cycif_tonsil_registered.ome.tif" } 'quantification' { - markers = "${params.nf_core_test_data_base}/data/imaging/quantification/markers.csv" - image = "${params.nf_core_test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif" - mask = "${params.nf_core_test_data_base}/data/imaging/quantification/cell.ome.tif" + markers = "${params.test_data_base}/data/imaging/quantification/markers.csv" + image = "${params.test_data_base}/data/imaging/quantification/cycif_tonsil_registered.ome.tif" + mask = "${params.test_data_base}/data/imaging/quantification/cell.ome.tif" } 'downstream' { - markers = "${params.nf_core_test_data_base}/data/imaging/downstream/markers.csv" - cell_feature_array = "${params.nf_core_test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv" + markers = "${params.test_data_base}/data/imaging/downstream/markers.csv" + cell_feature_array = "${params.test_data_base}/data/imaging/downstream/cycif_tonsil_cell.csv" } 'background_subtraction' { - markers = "${params.nf_core_test_data_base}/data/imaging/background_subtraction/markers.csv" - image = "${params.nf_core_test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif" + markers = "${params.test_data_base}/data/imaging/background_subtraction/markers.csv" + image = "${params.test_data_base}/data/imaging/background_subtraction/cycif_tonsil_registered.ome.tif" } 'core_detection' { - image = "${params.nf_core_test_data_base}/data/imaging/core_detection/single_core_dapi.tif" + image = "${params.test_data_base}/data/imaging/core_detection/single_core_dapi.tif" } } } diff --git a/nf-test.config b/nf-test.config index 3ba80fb..1848e92 100644 --- a/nf-test.config +++ b/nf-test.config @@ -6,5 +6,5 @@ config { workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" + configFile "tests/nextflow.config" } diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap index cc2128c..fbfee37 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -11,7 +11,7 @@ { "id": "test" }, - "test.gbk.gz:md5,e719cd124ccca0524df508cd178e853e" + "test.gbk.gz:md5,b40671a0001cb0b57187c23ca27db09d" ] ], "2": [ @@ -35,7 +35,7 @@ { "id": "test" }, - "test.gbk.gz:md5,e719cd124ccca0524df508cd178e853e" + "test.gbk.gz:md5,b40671a0001cb0b57187c23ca27db09d" ] ], "versions": [ @@ -44,6 +44,10 @@ ] } ], - "timestamp": "2024-01-24T14:00:39.927815714" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T12:46:38.299696892" } -} +} \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 0000000..4057647 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,35 @@ +params { + // Resource requests for nf-tests + max_cpus = 4 + max_memory = '16.GB' + max_time = '6.h' + + // Input data + input = 'https://github.com/nf-core/test-datasets/raw/phageannotator/assets/1.0.0/test_samplesheet.csv' + + // Tool options + reference_virus_fasta = 'https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz' + mash_screen_min_score = 0 + genomad_splits = 5 + + // Pipeline options + publish_dir_mode = 'symlink' + + // Test data base paths + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=23.04.0' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } + +// Load test_data.config +includeConfig '../conf/test_data.config' diff --git a/workflows/phageannotator/tests/skip_iphop.nf.test.snap b/workflows/phageannotator/tests/skip_iphop.nf.test.snap index 6d11f4e..8568cf2 100644 --- a/workflows/phageannotator/tests/skip_iphop.nf.test.snap +++ b/workflows/phageannotator/tests/skip_iphop.nf.test.snap @@ -125,7 +125,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -135,6 +134,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -218,7 +218,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -228,6 +227,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -274,6 +274,10 @@ ] } ], - "timestamp": "2024-02-01T11:51:49.427932984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T11:31:15.186440778" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap index b4c696c..180cc66 100644 --- a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap +++ b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap @@ -122,7 +122,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -130,6 +129,7 @@ "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -221,7 +221,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -229,6 +228,7 @@ "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -264,6 +264,10 @@ ] } ], - "timestamp": "2024-02-01T15:00:37.195786662" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T12:33:16.637666484" } } \ No newline at end of file From f6b3620c4d2186511e3694dafcd361a2b2b18dca Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 14 Feb 2024 12:52:00 -0800 Subject: [PATCH 13/23] Updated resource requests --- nextflow.config | 2 -- tests/nextflow.config | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index a54dda2..4acd300 100644 --- a/nextflow.config +++ b/nextflow.config @@ -137,8 +137,6 @@ params { } -includeConfig 'conf/test_data.config' - // Load base.config by default for all pipelines includeConfig 'conf/base.config' diff --git a/tests/nextflow.config b/tests/nextflow.config index 4057647..b0f0aa7 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -1,7 +1,7 @@ params { // Resource requests for nf-tests max_cpus = 4 - max_memory = '16.GB' + max_memory = '12.GB' max_time = '6.h' // Input data From 800fca7bdf758b8d18e00f15289806dd7ae5b699 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 14 Feb 2024 14:14:16 -0800 Subject: [PATCH 14/23] Updated failing sketches --- .../tests/main.nf.test.snap | 14 +++++++++----- .../tests/sketch_provided.nf.test.snap | 10 +++++++--- tests/main.nf.test.snap | 2 +- tests/nextflow.config | 2 +- .../tests/skip_reference_containment.nf.test.snap | 10 +++++++--- .../tests/skip_virus_clustering.nf.test.snap | 10 +++++++--- 6 files changed, 32 insertions(+), 16 deletions(-) diff --git a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test.snap b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test.snap index 61c74e5..905bd9e 100644 --- a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test.snap +++ b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/main.nf.test.snap @@ -7,13 +7,13 @@ { "id": "test2" }, - "test2.screen:md5,f4bfb5bdeab99353236ebf8100911405" + "test2.screen:md5,a50700d95a3bc0c9913997f142817bbd" ], [ { "id": "test" }, - "test.screen:md5,77858d67f1513d5883d1d1aa22f48629" + "test.screen:md5,9cd27acafbf63f1fa92e26c3e83bfa3e" ] ], "1": [ @@ -27,13 +27,13 @@ { "id": "test2" }, - "test2.screen:md5,f4bfb5bdeab99353236ebf8100911405" + "test2.screen:md5,a50700d95a3bc0c9913997f142817bbd" ], [ { "id": "test" }, - "test.screen:md5,77858d67f1513d5883d1d1aa22f48629" + "test.screen:md5,9cd27acafbf63f1fa92e26c3e83bfa3e" ] ], "versions": [ @@ -44,6 +44,10 @@ ] } ], - "timestamp": "2023-12-04T12:35:32.588786845" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T14:03:12.481182772" } } \ No newline at end of file diff --git a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test.snap b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test.snap index f192c05..6aae9b0 100644 --- a/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test.snap +++ b/subworkflows/local/fastq_fasta_reference_containment_mash/tests/sketch_provided.nf.test.snap @@ -13,7 +13,7 @@ { "id": "test" }, - "test.screen:md5,2d7ddb331f2c0c07e927adc8685e3deb" + "test.screen:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -32,7 +32,7 @@ { "id": "test" }, - "test.screen:md5,2d7ddb331f2c0c07e927adc8685e3deb" + "test.screen:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -42,6 +42,10 @@ ] } ], - "timestamp": "2023-12-04T13:20:53.978507251" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T14:03:25.561022329" } } \ No newline at end of file diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index be71653..2043ad6 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -97,6 +97,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-09T13:37:29.504208615" + "timestamp": "2024-02-14T14:13:15.109844835" } } \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config index b0f0aa7..e20405a 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -1,7 +1,7 @@ params { // Resource requests for nf-tests max_cpus = 4 - max_memory = '12.GB' + max_memory = '14.GB' max_time = '6.h' // Input data diff --git a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap index f761ed9..c980ee1 100644 --- a/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap +++ b/workflows/phageannotator/tests/skip_reference_containment.nf.test.snap @@ -132,7 +132,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -141,6 +140,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -231,7 +231,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,8aebba726df29aad131772449019ee78", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", @@ -240,6 +239,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -286,6 +286,10 @@ ] } ], - "timestamp": "2024-02-01T14:08:46.916902313" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T13:48:17.848127992" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap b/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap index 3cd5879..6d79a6e 100644 --- a/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap +++ b/workflows/phageannotator/tests/skip_virus_clustering.nf.test.snap @@ -140,7 +140,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -151,6 +150,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -250,7 +250,6 @@ "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a6aa8efc5dbcafe7129f58ed120eaa93", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", @@ -261,6 +260,7 @@ "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", + "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -308,6 +308,10 @@ ] } ], - "timestamp": "2024-02-01T15:21:27.006208845" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T13:59:39.771250096" } } \ No newline at end of file From a7aa0a5bfd6be3a4211638b7a6043c41117bda4d Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Wed, 14 Feb 2024 15:52:38 -0800 Subject: [PATCH 15/23] Updated resource requests in nf-test config --- .../tests/main.nf.test | 2 +- tests/nextflow.config | 14 +++++++++----- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test b/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test index b92fbe9..58d5b8d 100644 --- a/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test +++ b/subworkflows/local/fasta_virus_classification_genomad/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { when { params { - outdir = "$outputDir" + genomad_splits = 5 } workflow { """ diff --git a/tests/nextflow.config b/tests/nextflow.config index e20405a..30d394d 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -1,9 +1,4 @@ params { - // Resource requests for nf-tests - max_cpus = 4 - max_memory = '14.GB' - max_time = '6.h' - // Input data input = 'https://github.com/nf-core/test-datasets/raw/phageannotator/assets/1.0.0/test_samplesheet.csv' @@ -20,6 +15,15 @@ params { modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' } +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 4 + memory = 15.GB + time = 2.h + } +} + // Impose same minimum Nextflow version as the pipeline for testing manifest { nextflowVersion = '!>=23.04.0' From ae7221d5dd8559e4893fedfd421e51e5a1f3e9dc Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 15 Feb 2024 11:21:18 -0800 Subject: [PATCH 16/23] Fixed pharokka and samtools/sort snapshots --- modules.json | 14 +- .../nf-core/samtools/flagstat/environment.yml | 4 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test | 36 +++ .../samtools/flagstat/tests/main.nf.test.snap | 32 ++ .../nf-core/samtools/flagstat/tests/tags.yml | 2 + .../nf-core/samtools/idxstats/environment.yml | 4 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test | 36 +++ .../samtools/idxstats/tests/main.nf.test.snap | 32 ++ .../nf-core/samtools/idxstats/tests/tags.yml | 2 + .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/csi.nextflow.config | 7 + .../nf-core/samtools/index/tests/main.nf.test | 87 ++++++ .../samtools/index/tests/main.nf.test.snap | 74 +++++ modules/nf-core/samtools/index/tests/tags.yml | 2 + modules/nf-core/samtools/sort/environment.yml | 4 +- modules/nf-core/samtools/sort/main.nf | 4 +- .../nf-core/samtools/sort/tests/main.nf.test | 33 +-- .../samtools/sort/tests/main.nf.test.snap | 47 ++- .../nf-core/samtools/stats/environment.yml | 4 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../nf-core/samtools/stats/tests/main.nf.test | 55 ++-- .../samtools/stats/tests/main.nf.test.snap | 32 +- .../tests/main.nf.test.snap | 14 +- .../tests/main.nf.test | 28 +- .../tests/main.nf.test.snap | 36 ++- .../bam_stats_samtools/tests/main.nf.test | 108 +++++++ .../tests/main.nf.test.snap | 164 +++++++++++ .../nf-core/bam_stats_samtools/tests/tags.yml | 2 + tests/nextflow.config | 15 +- .../tests/skip_genomad.nf.test.snap | 277 ------------------ 33 files changed, 765 insertions(+), 410 deletions(-) create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/flagstat/tests/tags.yml create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/idxstats/tests/tags.yml create mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/index/tests/tags.yml create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/tags.yml delete mode 100644 workflows/phageannotator/tests/skip_genomad.nf.test.snap diff --git a/modules.json b/modules.json index e4c4180..3969855 100644 --- a/modules.json +++ b/modules.json @@ -125,27 +125,27 @@ }, "samtools/flagstat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/sort": { "branch": "master", - "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "untar": { @@ -159,12 +159,12 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["fastq_align_bowtie2"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_sort_stats_samtools"] }, "fastq_align_bowtie2": { diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 04c82f1..bd57cb5 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,8 @@ +name: samtools_flagstat channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 9dee35a..eb5f525 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test new file mode 100644 index 0000000..24c3c04 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FLAGSTAT" + script "../main.nf" + process "SAMTOOLS_FLAGSTAT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/flagstat" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.flagstat).match("flagstat") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap new file mode 100644 index 0000000..a76fc27 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -0,0 +1,32 @@ +{ + "flagstat": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:31:37.783927" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,fd0030ce49ab3a92091ad80260226452" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:44.299617452" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml new file mode 100644 index 0000000..2d2b725 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 04c82f1..174973b 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,8 @@ +name: samtools_idxstats channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index b22d084..a544026 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test new file mode 100644 index 0000000..a2dcb27 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_IDXSTATS" + script "../main.nf" + process "SAMTOOLS_IDXSTATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/idxstats" + + test("bam") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.idxstats).match("idxstats") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap new file mode 100644 index 0000000..a7050bd --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -0,0 +1,32 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,613dde56f108418039ffcdeeddba397a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:50.147462763" + }, + "idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:36:41.561026" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml new file mode 100644 index 0000000..d3057c6 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 04c82f1..a5e5064 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,8 @@ +name: samtools_index channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 256bd7c..dc14f98 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 0000000..0ed260e --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 0000000..bb7756d --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("bai") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert snapshot(process.out.versions).match("bai_versions") } + ) + } + } + + test("crai") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert snapshot(process.out.versions).match("crai_versions") } + ) + } + } + + test("csi") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert snapshot(process.out.versions).match("csi_versions") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 0000000..3dc8e7d --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "crai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:00.324667957" + }, + "csi_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:07.885103162" + }, + "crai": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:41:38.446424" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:40:46.579747" + }, + "bai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:51.641425452" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 0000000..e0f58a7 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index f4064b7..4d898e4 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 4a666d4..cdd8305 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index abb8097..31e24b8 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/sort" - test("test_samtools_sort") { + test("bam") { config "./nextflow.config" @@ -18,12 +18,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) """ } } @@ -34,10 +32,9 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - test("test_samtools_sort_stub") { + test("bam_stub") { config "./nextflow.config" options "-stub-run" @@ -48,12 +45,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) """ } } @@ -61,13 +56,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } ) } - } - } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index ff72225..a7cf021 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,5 +1,27 @@ { - "test_samtools_sort": { + "bam_stub_bam": { + "content": [ + "test.sorted.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:21:04.364044" + }, + "bam_stub_versions": { + "content": [ + [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:00.20800281" + }, + "bam": { "content": [ { "0": [ @@ -8,14 +30,14 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,c6ea1346ec4aae007eb40b708935088c" ] ], "1": [ ], "2": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ], "bam": [ [ @@ -23,26 +45,21 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,c6ea1346ec4aae007eb40b708935088c" ] ], "csi": [ ], "versions": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ] } ], - "timestamp": "2023-12-04T11:11:22.005628301" - }, - "test_samtools_sort_stub": { - "content": [ - "test.sorted.bam", - [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" - ] - ], - "timestamp": "2023-12-04T17:47:22.314445935" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:14:52.736359271" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 04c82f1..67bb0ca 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,8 @@ +name: samtools_stats channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 07286ef..52b00f4 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e037132..e3d5cb1 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,75 +4,62 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" tag "modules" - tag "modules/nf-core" + tag "modules_nfcore" tag "samtools" tag "samtools/stats" - test("SAMTOOLS STATS Should run without failures") { + test("bam") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here. - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) input[1] = [[],[]] """ - } } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - test("SAMTOOLS CRAM Should run without failures") { + test("cram") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) - - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) """ } - - } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - - } diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 516b2b0..1b7c9ba 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "SAMTOOLS STATS Should run without failures": { + "cram": { "content": [ { "0": [ @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -20,17 +20,21 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-10-18T12:12:42.998746" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:25.562429714" }, - "SAMTOOLS CRAM Should run without failures": { + "bam": { "content": [ { "0": [ @@ -39,11 +43,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -51,14 +55,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-10-18T12:13:30.747222" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:07.857611509" } } \ No newline at end of file diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap index fbfee37..560e2ee 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -9,15 +9,15 @@ "1": [ [ { - "id": "test" + "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" }, - "test.gbk.gz:md5,b40671a0001cb0b57187c23ca27db09d" + "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" ] ], "2": [ [ { - "id": "test" + "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" }, "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" ] @@ -25,7 +25,7 @@ "pharokka_final_output_tsv": [ [ { - "id": "test" + "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" }, "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" ] @@ -33,9 +33,9 @@ "pharokka_gbk_gz": [ [ { - "id": "test" + "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" }, - "test.gbk.gz:md5,b40671a0001cb0b57187c23ca27db09d" + "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" ] ], "versions": [ @@ -48,6 +48,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T12:46:38.299696892" + "timestamp": "2024-02-15T09:55:43.577714482" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 59b749d..75b5b93 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -24,12 +24,14 @@ nextflow_workflow { } workflow { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -54,12 +56,14 @@ nextflow_workflow { } workflow { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 6dafc3b..6645a09 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -11,6 +11,10 @@ ] ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, "timestamp": "2023-10-22T20:25:03.687121177" }, "test_bam_sort_stats_samtools_paired_end_idxstats": { @@ -25,6 +29,10 @@ ] ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, "timestamp": "2023-10-22T20:25:03.709648916" }, "test_bam_sort_stats_samtools_single_end_stats": { @@ -35,11 +43,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,796f45f791f06291b76329528fae0a54" + "test.stats:md5,cb0bf2b79de52fdf0c61e80efcdb0bb4" ] ] ], - "timestamp": "2023-10-22T20:25:58.398627806" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:38.553256801" }, "test_bam_sort_stats_samtools_paired_end_stats": { "content": [ @@ -49,11 +61,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" + "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" ] ] ], - "timestamp": "2023-10-22T20:25:03.644306159" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:48.355870518" }, "test_bam_sort_stats_samtools_single_end_idxstats": { "content": [ @@ -67,7 +83,11 @@ ] ] ], - "timestamp": "2023-10-22T20:25:58.451364604" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.84631" }, "test_bam_sort_stats_samtools_single_end_flagstats": { "content": [ @@ -81,6 +101,10 @@ ] ] ], - "timestamp": "2023-10-22T20:25:58.416859285" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.829756" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test new file mode 100644 index 0000000..c8b21f2 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_workflow { + + name "Test Workflow BAM_STATS_SAMTOOLS" + script "../main.nf" + workflow "BAM_STATS_SAMTOOLS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_stats_samtools" + tag "subworkflows/bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/stats" + + test("test_bam_stats_samtools_single_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end_cram") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap new file mode 100644 index 0000000..bf0b0c6 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -0,0 +1,164 @@ +{ + "test_bam_stats_samtools_paired_end_cram_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:31:26.194017574" + }, + "test_bam_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,ddaf8f33fe9c1ebe9b06933213aec8ed" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:45:06.230091746" + }, + "test_bam_stats_samtools_paired_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:17:27.717482" + }, + "test_bam_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:26:10.340046381" + }, + "test_bam_stats_samtools_paired_end_cram_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:31:26.207052003" + }, + "test_bam_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,dc178e1a4956043aba8abc83e203521b" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:57.442208382" + }, + "test_bam_stats_samtools_paired_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:17:27.726719" + }, + "test_bam_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:26:10.349439801" + }, + "test_bam_stats_samtools_paired_end_cram_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d3345c4887f4a9ea4f7f56405b495db0" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:45:14.997164209" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml new file mode 100644 index 0000000..ec2f2d6 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_stats_samtools: + - subworkflows/nf-core/bam_stats_samtools/** diff --git a/tests/nextflow.config b/tests/nextflow.config index 30d394d..8652344 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -18,9 +18,18 @@ params { // Impose sensible resource limits for testing process { withName: '.*' { - cpus = 4 - memory = 15.GB - time = 2.h + max_cpus = 4 + max_memory = 15.GB + max_time = 2.h + } + + withName: SAMTOOLS_SORT { + cpus = 2 + ext.prefix = null + } + + withName: SAMTOOLS_STATS { + cpus = 2 } } diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test.snap b/workflows/phageannotator/tests/skip_genomad.nf.test.snap deleted file mode 100644 index 46ea832..0000000 --- a/workflows/phageannotator/tests/skip_genomad.nf.test.snap +++ /dev/null @@ -1,277 +0,0 @@ -{ - "Parameters: skip_genomad = true": { - "content": [ - { - "0": [ - [ - { - "id": "test2" - }, - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" - ], - [ - { - 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"versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", - "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", - "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", - "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", - "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", - "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", - "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", - "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", - "versions.yml:md5,755876cdfeb32585833c108ed6635839", - "versions.yml:md5,755876cdfeb32585833c108ed6635839", - "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", - "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", - "versions.yml:md5,76fc7f1f019facce5a0af4d78f01c624", - "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", - "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", - "versions.yml:md5,8aebba726df29aad131772449019ee78", - "versions.yml:md5,987d2e54a85311b917599dc41c90418c", - "versions.yml:md5,a856eefde99260259440d942c1d56ff4", - "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", - "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", - "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", - "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", - "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", - "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" - ], - "virus_classification_tsv": [ - - ], - "virus_enrichment_tsv": [ - [ - { - "id": "test2" - }, - "test2.viromeqc.tsv:md5,728ab79cbb6c7afd0dc3f38c5ddfe642" - ], - [ - { - "id": "test" - }, - "test.viromeqc.tsv:md5,b55f2c77b63adc41da980568819d1aae" - ] - ], - "virus_quality_tsv": [ - [ - { - "id": "test2" - }, - "test2_quality_summary.tsv:md5,134567fa42775bd31cc4c59e9e3b1e95" - ], - [ - { - "id": "test" - }, - "test_quality_summary.tsv:md5,162b77bec682c86854b973563674ee01" - ] - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-12T10:55:05.591614887" - } -} \ No newline at end of file From 8ed230dfa7ee25cc38d266ef580eeede79d85b97 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 15 Feb 2024 11:24:04 -0800 Subject: [PATCH 17/23] Limited resources --- tests/nextflow.config | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/tests/nextflow.config b/tests/nextflow.config index 8652344..439a638 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -10,6 +10,11 @@ params { // Pipeline options publish_dir_mode = 'symlink' + // Resource limiting + max_cpus = 4 + max_memory = '15.GB' + max_time = '6.h' + // Test data base paths test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules' modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' @@ -17,12 +22,6 @@ params { // Impose sensible resource limits for testing process { - withName: '.*' { - max_cpus = 4 - max_memory = 15.GB - max_time = 2.h - } - withName: SAMTOOLS_SORT { cpus = 2 ext.prefix = null From 202304f715286489b8960388626b31db7335b8c6 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 15 Feb 2024 11:53:51 -0800 Subject: [PATCH 18/23] Removed samtools_sort prefix only in bam_sort_stats_samtools tests --- .../nf-core/bam_sort_stats_samtools/tests/main.nf.test | 1 + .../nf-core/bam_sort_stats_samtools/tests/nextflow.config | 5 +++++ tests/nextflow.config | 1 - 3 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/tests/nextflow.config diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 75b5b93..98d2f5c 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_workflow { name "Test Workflow BAM_SORT_STATS_SAMTOOLS" script "../main.nf" workflow "BAM_SORT_STATS_SAMTOOLS" + config "./nextflow.config" tag "subworkflows" tag "subworkflows_nfcore" tag "subworkflows/bam_sort_stats_samtools" diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/nextflow.config b/subworkflows/nf-core/bam_sort_stats_samtools/tests/nextflow.config new file mode 100644 index 0000000..6b00fae --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SAMTOOLS_SORT { + ext.prefix = null + } +} diff --git a/tests/nextflow.config b/tests/nextflow.config index 439a638..9ae5810 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -24,7 +24,6 @@ params { process { withName: SAMTOOLS_SORT { cpus = 2 - ext.prefix = null } withName: SAMTOOLS_STATS { From bf661dab04adc4fe00455d8e4646bdba8b7939df Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Thu, 15 Feb 2024 12:21:24 -0800 Subject: [PATCH 19/23] Updated fasta_phage_function_pharokka snap --- .../tests/main.nf.test.snap | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap index 560e2ee..007455c 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "1": [ [ { - "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" + "id": "test" }, "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" ] @@ -17,7 +17,7 @@ "2": [ [ { - "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" + "id": "test" }, "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" ] @@ -25,7 +25,7 @@ "pharokka_final_output_tsv": [ [ { - "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" + "id": "test" }, "test_cds_final_merged_output.tsv:md5,1242b6ffe6e53ef5bce0a9a2cac3cd45" ] @@ -33,7 +33,7 @@ "pharokka_gbk_gz": [ [ { - "id": "test:md5,6ac4cfdabe914505778956bc94bbed83" + "id": "test" }, "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" ] @@ -48,6 +48,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-15T09:55:43.577714482" + "timestamp": "2024-02-15T12:17:44.339900336" } } \ No newline at end of file From 5cb010168a83ac53e81e49fe78e083a0d8151aa9 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Fri, 16 Feb 2024 07:29:10 -0800 Subject: [PATCH 20/23] Updated nf-tests for local running and modified resource requests --- .gitignore | 3 + .../anicluster/anicalc/tests/main.nf.test | 2 +- .../local/anicluster/anicalc/tests/tags.yml | 2 +- .../anicluster/aniclust/tests/main.nf.test | 2 +- .../local/anicluster/aniclust/tests/tags.yml | 2 +- .../anicluster/extractreps/tests/main.nf.test | 2 +- .../anicluster/extractreps/tests/tags.yml | 2 +- .../local/coverm/contig/tests/main.nf.test | 2 +- modules/local/coverm/contig/tests/tags.yml | 2 +- modules/local/instrain/stb/tests/main.nf.test | 2 +- modules/local/instrain/stb/tests/tags.yml | 2 +- modules/local/mash/paste/tests/main.nf.test | 2 +- modules/local/mash/paste/tests/tags.yml | 2 +- modules/local/seqkit/seq/tests/main.nf.test | 2 +- modules/local/seqkit/seq/tests/tags.yml | 2 +- .../local/viromeqc/install/tests/main.nf.test | 2 +- modules/local/viromeqc/install/tests/tags.yml | 2 +- .../viromeqc/viromeqc/tests/main.nf.test | 4 +- .../local/viromeqc/viromeqc/tests/tags.yml | 2 +- .../nf-core/checkv/downloaddatabase/main.nf | 2 + modules/nf-core/genomad/download/main.nf | 2 + .../tests/tags.yml | 2 + tests/main.nf.test | 2 + tests/main.nf.test.snap | 4 +- .../phageannotator/tests/main.nf.test.snap | 30 +- .../tests/skip_bacphlip.nf.test.snap | 30 +- .../tests/skip_checkv.nf.test.snap | 30 +- .../tests/skip_genomad.nf.test.snap | 277 ++++++++++++++++++ .../tests/skip_genomad_taxonomy.nf.test.snap | 30 +- .../tests/skip_instrain.nf.test.snap | 30 +- .../tests/skip_iphop.nf.test.snap | 30 +- .../tests/skip_pharokka.nf.test.snap | 30 +- .../skip_reference_containment.nf.test.snap | 30 +- .../tests/skip_viromeqc.nf.test.snap | 30 +- .../tests/skip_virus_clustering.nf.test.snap | 34 +-- 35 files changed, 461 insertions(+), 173 deletions(-) create mode 100644 subworkflows/local/fasta_microdiversity_instrain/tests/tags.yml create mode 100644 workflows/phageannotator/tests/skip_genomad.nf.test.snap diff --git a/.gitignore b/.gitignore index 5ef6e6d..8113c25 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,6 @@ testing* .nf-test* test.xml nf-test-checklist.csv +*parallel-nf-test.sh +nf-test-parallel/ + diff --git a/modules/local/anicluster/anicalc/tests/main.nf.test b/modules/local/anicluster/anicalc/tests/main.nf.test index 0835629..3b967e1 100644 --- a/modules/local/anicluster/anicalc/tests/main.nf.test +++ b/modules/local/anicluster/anicalc/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_process { tag "modules" tag "modules_local" tag "anicluster" - tag "anicluster/anicalc" + tag "anicluster_anicalc" test("['modules_local']['blast_txt']") { diff --git a/modules/local/anicluster/anicalc/tests/tags.yml b/modules/local/anicluster/anicalc/tests/tags.yml index 5130c5b..de4dd3f 100644 --- a/modules/local/anicluster/anicalc/tests/tags.yml +++ b/modules/local/anicluster/anicalc/tests/tags.yml @@ -1,2 +1,2 @@ -anicluster/anicalc: +anicluster_anicalc: - modules/local/anicluster/anicalc/** diff --git a/modules/local/anicluster/aniclust/tests/main.nf.test b/modules/local/anicluster/aniclust/tests/main.nf.test index 84e2407..2cd6233 100644 --- a/modules/local/anicluster/aniclust/tests/main.nf.test +++ b/modules/local/anicluster/aniclust/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_process { tag "modules" tag "modules_local" tag "anicluster" - tag "anicluster/aniclust" + tag "anicluster_aniclust" test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['ani_tsv']") { diff --git a/modules/local/anicluster/aniclust/tests/tags.yml b/modules/local/anicluster/aniclust/tests/tags.yml index 1d720df..c51931a 100644 --- a/modules/local/anicluster/aniclust/tests/tags.yml +++ b/modules/local/anicluster/aniclust/tests/tags.yml @@ -1,2 +1,2 @@ -anicluster/aniclust: +anicluster_aniclust: - modules/local/anicluster/aniclust/** diff --git a/modules/local/anicluster/extractreps/tests/main.nf.test b/modules/local/anicluster/extractreps/tests/main.nf.test index 8c46965..c2f10bc 100644 --- a/modules/local/anicluster/extractreps/tests/main.nf.test +++ b/modules/local/anicluster/extractreps/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_process { tag "modules" tag "modules_local" tag "anicluster" - tag "anicluster/extractreps" + tag "anicluster_extractreps" test("['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'] & ['modules_local']['clusters_tsv']") { diff --git a/modules/local/anicluster/extractreps/tests/tags.yml b/modules/local/anicluster/extractreps/tests/tags.yml index 6aff4bf..a3ec13c 100644 --- a/modules/local/anicluster/extractreps/tests/tags.yml +++ b/modules/local/anicluster/extractreps/tests/tags.yml @@ -1,2 +1,2 @@ -anicluster/extractreps: +anicluster_extractreps: - modules/local/anicluster/extractreps/** diff --git a/modules/local/coverm/contig/tests/main.nf.test b/modules/local/coverm/contig/tests/main.nf.test index eebf10a..1777205 100644 --- a/modules/local/coverm/contig/tests/main.nf.test +++ b/modules/local/coverm/contig/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "COVERM_CONTIG" tag "modules" tag "modules_local" - tag "coverm/contig" + tag "coverm_contig" test("['bacteroides_fragilis']['illumina']['test1_paired_end_bam'] & ['bacteroides_fragilis']['illumina']['test2_paired_end_bam']") { diff --git a/modules/local/coverm/contig/tests/tags.yml b/modules/local/coverm/contig/tests/tags.yml index dc354e3..0e62aee 100644 --- a/modules/local/coverm/contig/tests/tags.yml +++ b/modules/local/coverm/contig/tests/tags.yml @@ -1,2 +1,2 @@ -coverm/contig: +coverm_contig: - modules/local/coverm/contig/** diff --git a/modules/local/instrain/stb/tests/main.nf.test b/modules/local/instrain/stb/tests/main.nf.test index b19bb40..66601ae 100644 --- a/modules/local/instrain/stb/tests/main.nf.test +++ b/modules/local/instrain/stb/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "INSTRAIN_STB" tag "modules" tag "modules_local" - tag "instrain/stb" + tag "instrain_stb" test("['homo_sapiens']['genome']['genome_fasta']") { diff --git a/modules/local/instrain/stb/tests/tags.yml b/modules/local/instrain/stb/tests/tags.yml index 65c90e5..8235802 100644 --- a/modules/local/instrain/stb/tests/tags.yml +++ b/modules/local/instrain/stb/tests/tags.yml @@ -1,2 +1,2 @@ -instrain/stb: +instrain_stb: - modules/local/instrain/stb/** diff --git a/modules/local/mash/paste/tests/main.nf.test b/modules/local/mash/paste/tests/main.nf.test index 7c409cc..015c998 100644 --- a/modules/local/mash/paste/tests/main.nf.test +++ b/modules/local/mash/paste/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "MASH_PASTE" tag "modules" tag "modules_local" - tag "mash/paste" + tag "mash_paste" test("['modules_local']['mash_sketch1_msh'] & ['modules_local']['mash_sketch2_msh']") { diff --git a/modules/local/mash/paste/tests/tags.yml b/modules/local/mash/paste/tests/tags.yml index 3f23ef6..17d5a68 100644 --- a/modules/local/mash/paste/tests/tags.yml +++ b/modules/local/mash/paste/tests/tags.yml @@ -1,2 +1,2 @@ -mash/paste: +mash_paste: - modules/local/mash/paste/** diff --git a/modules/local/seqkit/seq/tests/main.nf.test b/modules/local/seqkit/seq/tests/main.nf.test index 24d337b..5b4a1c4 100644 --- a/modules/local/seqkit/seq/tests/main.nf.test +++ b/modules/local/seqkit/seq/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "SEQKIT_SEQ" tag "modules" tag "modules_local" - tag "seqkit/seq" + tag "seqkit_seq" test("['modules_local']['assembly_fasta_gz']") { diff --git a/modules/local/seqkit/seq/tests/tags.yml b/modules/local/seqkit/seq/tests/tags.yml index 584179b..2d971c3 100644 --- a/modules/local/seqkit/seq/tests/tags.yml +++ b/modules/local/seqkit/seq/tests/tags.yml @@ -1,2 +1,2 @@ -seqkit/seq: +seqkit_seq: - modules/local/seqkit/seq/** diff --git a/modules/local/viromeqc/install/tests/main.nf.test b/modules/local/viromeqc/install/tests/main.nf.test index 7975280..3b93d96 100644 --- a/modules/local/viromeqc/install/tests/main.nf.test +++ b/modules/local/viromeqc/install/tests/main.nf.test @@ -5,7 +5,7 @@ nextflow_process { process "VIROMEQC_INSTALL" tag "modules" tag "modules_local" - tag "viromeqc/install" + tag "viromeqc_install" test("No input required") { diff --git a/modules/local/viromeqc/install/tests/tags.yml b/modules/local/viromeqc/install/tests/tags.yml index 3042933..3b019f4 100644 --- a/modules/local/viromeqc/install/tests/tags.yml +++ b/modules/local/viromeqc/install/tests/tags.yml @@ -1,2 +1,2 @@ -viromeqc/install: +viromeqc_install: - modules/local/viromeqc/install/** diff --git a/modules/local/viromeqc/viromeqc/tests/main.nf.test b/modules/local/viromeqc/viromeqc/tests/main.nf.test index 91c457f..413f848 100644 --- a/modules/local/viromeqc/viromeqc/tests/main.nf.test +++ b/modules/local/viromeqc/viromeqc/tests/main.nf.test @@ -5,8 +5,8 @@ nextflow_process { process "VIROMEQC_VIROMEQC" tag "modules" tag "modules_local" - tag "viromeqc/viromeqc" - tag "viromeqc/install" + tag "viromeqc_viromeqc" + tag "viromeqc_install" test("sarscov2 - illumina - test_1_fastq_gz") { setup { diff --git a/modules/local/viromeqc/viromeqc/tests/tags.yml b/modules/local/viromeqc/viromeqc/tests/tags.yml index e95aa16..376f0c1 100644 --- a/modules/local/viromeqc/viromeqc/tests/tags.yml +++ b/modules/local/viromeqc/viromeqc/tests/tags.yml @@ -1,2 +1,2 @@ -viromeqc/viromeqc: +viromeqc_viromeqc: - modules/local/viromeqc/viromeqc/** diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index bc5086f..2043d55 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,6 +18,8 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index a2ac6ec..632d494 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,6 +16,8 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ + https_proxy=http://klone-dip1-A-ib:3128 + export https_proxy genomad \\ download-database . diff --git a/subworkflows/local/fasta_microdiversity_instrain/tests/tags.yml b/subworkflows/local/fasta_microdiversity_instrain/tests/tags.yml new file mode 100644 index 0000000..80d112f --- /dev/null +++ b/subworkflows/local/fasta_microdiversity_instrain/tests/tags.yml @@ -0,0 +1,2 @@ +fasta_microdiversity_instrain: + - subworkflows/local/fasta_microdiversity_instrain/** diff --git a/tests/main.nf.test b/tests/main.nf.test index 9b1d055..8fc17df 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -17,6 +17,8 @@ nextflow_pipeline { genomad_sensitivity = 0.1 checkv_minimal_db = true iphop_partial_test = true + max_cpus = 4 + max_memory = '15.GB' } } diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 2043ad6..b6887e4 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -91,7 +91,7 @@ ], "test1.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", - "software_versions.yml:md5,d6a63054b92c6bd4cda093b3592e81e1" + "software_versions.yml:md5,3d2ea4a6e456777a0a77bd88676f1994" ], "meta": { "nf-test": "0.8.4", @@ -99,4 +99,4 @@ }, "timestamp": "2024-02-14T14:13:15.109844835" } -} \ No newline at end of file +} diff --git a/workflows/phageannotator/tests/main.nf.test.snap b/workflows/phageannotator/tests/main.nf.test.snap index 43c83ce..09f57d1 100644 --- a/workflows/phageannotator/tests/main.nf.test.snap +++ b/workflows/phageannotator/tests/main.nf.test.snap @@ -105,6 +105,8 @@ ] ], "9": [ + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", @@ -112,18 +114,16 @@ "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", + "versions.yml:md5,374c63bf7c31c6c34acbf8d74e6c7dcc", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,74b2068d24b17a2f4a097a3063da3dae", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", @@ -135,14 +135,14 @@ "versions.yml:md5,987d2e54a85311b917599dc41c90418c", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "anicluster_reps_fna_gz": [ @@ -206,6 +206,8 @@ ] ], "versions": [ + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", @@ -213,18 +215,16 @@ "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", + "versions.yml:md5,374c63bf7c31c6c34acbf8d74e6c7dcc", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", "versions.yml:md5,42ce3c1803e6f3030b60d1d4610b629d", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,74b2068d24b17a2f4a097a3063da3dae", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", @@ -236,14 +236,14 @@ "versions.yml:md5,987d2e54a85311b917599dc41c90418c", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -294,6 +294,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-09T15:49:14.848581359" + "timestamp": "2024-02-15T15:44:36.666475551" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap index fa7f50f..0828cc4 100644 --- a/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap +++ b/workflows/phageannotator/tests/skip_bacphlip.nf.test.snap @@ -105,6 +105,8 @@ ] ], "9": [ + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", @@ -112,17 +114,15 @@ "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", + "versions.yml:md5,374c63bf7c31c6c34acbf8d74e6c7dcc", "versions.yml:md5,3c8b8ac5a86d6d7fba86fc61f4d5fca9", - "versions.yml:md5,3d3432539468e0fae3b05d63cd5237d0", - "versions.yml:md5,4698f3f4cdba1748298d6fc664fe55d4", "versions.yml:md5,478c8fdcebf1357f40c26d7991d85eb4", "versions.yml:md5,5074b29ede738ba6d39ef056e1cde929", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", - "versions.yml:md5,57a9c1152c52dc32d2023ce8e2b939ab", "versions.yml:md5,5bf636608598d8b495d8b38fcee37dd0", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,6bf7a212d54ddc08bb3d6c7ce9f4cddb", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,74b2068d24b17a2f4a097a3063da3dae", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", @@ -134,14 +134,14 @@ "versions.yml:md5,987d2e54a85311b917599dc41c90418c", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", 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"virus_classification_tsv": [ @@ -290,6 +290,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T13:48:17.848127992" + "timestamp": "2024-02-15T16:02:07.204634331" } } \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap index 180cc66..21c276b 100644 --- a/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap +++ b/workflows/phageannotator/tests/skip_viromeqc.nf.test.snap @@ -94,6 +94,8 @@ ] ], "9": [ + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", "versions.yml:md5,00a12ed45ed179a55e30c05dbb3d31f3", "versions.yml:md5,04bf25e5231ce1f8077581bb7a2c07f4", "versions.yml:md5,0c310e8a973612ff99e0df847fb656ea", @@ -101,18 +103,16 @@ "versions.yml:md5,1439e948f383899aaccbf49506923b04", "versions.yml:md5,2b068b9678f63d6bb06a2a3652e92ba9", "versions.yml:md5,2d1864a0523e2738f150eaf87d4472d5", + 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"versions.yml:md5,755876cdfeb32585833c108ed6635839", "versions.yml:md5,769114e3bb009aceb4763a1a0fa80d5a", @@ -223,12 +223,12 @@ "versions.yml:md5,987d2e54a85311b917599dc41c90418c", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], "virus_classification_tsv": [ @@ -268,6 +268,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T12:33:16.637666484" + "timestamp": 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"versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -228,39 +228,39 @@ ] ], "versions": [ + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", + "versions.yml:md5,005aa3fca95c916b586f09b1c12aae6f", 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"versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", "versions.yml:md5,716410d7e9dc048a64ada71202cbc23e", + "versions.yml:md5,74b2068d24b17a2f4a097a3063da3dae", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,7e54b5f822df67b99faf67629e81963f", "versions.yml:md5,987d2e54a85311b917599dc41c90418c", "versions.yml:md5,a856eefde99260259440d942c1d56ff4", "versions.yml:md5,afc743a69ab04322fbc732b24e18d208", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,b6a0d868f5f2be1093be05fc0638008d", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", + "versions.yml:md5,bcf62c8c784b9f46c8372e86654cae6b", "versions.yml:md5,c0598196e761dbcdc90ff95a2f623b9c", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", - "versions.yml:md5,c7c1550786083ee8f3264b19ccf0fcbb", "versions.yml:md5,c97cb7740ce1aa3cf22cb6e8be2d62ce", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,d73a3ecea014f00c8d95513555c42d23", "versions.yml:md5,de688faac0a9124c4f2db74ce1b2c795", "versions.yml:md5,dfa7110695181c4e8daa47d384563588", - "versions.yml:md5,eabc04f1b3bfdaf113cf421fbc72672b", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6", "versions.yml:md5,f383a8d4db50b157e4a6a0ef4670fbc6" ], @@ -312,6 +312,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T13:59:39.771250096" + "timestamp": "2024-02-15T16:11:24.274930365" } } \ No newline at end of file From 147b318be9a4fad0d63fe969caecd76faab49060 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Fri, 16 Feb 2024 07:34:12 -0800 Subject: [PATCH 21/23] Removed local proxy code --- modules/nf-core/checkv/downloaddatabase/main.nf | 2 -- modules/nf-core/genomad/download/main.nf | 2 -- 2 files changed, 4 deletions(-) diff --git a/modules/nf-core/checkv/downloaddatabase/main.nf b/modules/nf-core/checkv/downloaddatabase/main.nf index 2043d55..bc5086f 100644 --- a/modules/nf-core/checkv/downloaddatabase/main.nf +++ b/modules/nf-core/checkv/downloaddatabase/main.nf @@ -18,8 +18,6 @@ process CHECKV_DOWNLOADDATABASE { prefix = task.ext.prefix ?: "checkv_db" """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy checkv download_database \\ $args \\ ./$prefix/ \\ diff --git a/modules/nf-core/genomad/download/main.nf b/modules/nf-core/genomad/download/main.nf index 632d494..a2ac6ec 100644 --- a/modules/nf-core/genomad/download/main.nf +++ b/modules/nf-core/genomad/download/main.nf @@ -16,8 +16,6 @@ process GENOMAD_DOWNLOAD { script: def args = task.ext.args ?: '' """ - https_proxy=http://klone-dip1-A-ib:3128 - export https_proxy genomad \\ download-database . From 7218318d003c8684c2ac3ec2bcda830c80fe5354 Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Fri, 16 Feb 2024 09:40:22 -0800 Subject: [PATCH 22/23] Reduce storage used by tests --- tests/main.nf.test | 22 +++++---- tests/main.nf.test.snap | 46 +++++++++---------- .../phageannotator/tests/skip_genomad.nf.test | 24 +++++----- .../tests/skip_genomad.nf.test.snap | 38 +++++++-------- 4 files changed, 67 insertions(+), 63 deletions(-) diff --git a/tests/main.nf.test b/tests/main.nf.test index 8fc17df..f763093 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -9,16 +9,18 @@ nextflow_pipeline { test("Parameters: default") { when { params { - outdir = "$outputDir" - mash_screen_min_score = 0.5 - genomad_min_score = 0.01 - genomad_max_fdr = 1 - genomad_disable_nn = true - genomad_sensitivity = 0.1 - checkv_minimal_db = true - iphop_partial_test = true - max_cpus = 4 - max_memory = '15.GB' + outdir = "$outputDir" + mash_screen_min_score = 1 + mash_screen_winner_take_all = true + genomad_min_score = 0.01 + genomad_max_fdr = 1 + genomad_disable_nn = true + genomad_sensitivity = 0.1 + checkv_minimal_db = true + checkv_min_length = 3000 + iphop_partial_test = true + max_cpus = 4 + max_memory = '15.GB' } } diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index b6887e4..42a9cc8 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -19,13 +19,13 @@ ], [ [ - "test1.fasta_w_screen_hits.fna.gz:md5,e93c24be014c9bb221dc97caf118ad61", - "test2.fasta_w_screen_hits.fna.gz:md5,21a504e49b0bf3547604573aef34d6c1" + "test1.fasta_w_screen_hits.fna.gz:md5,8dff8263a5cc85fe5c816b208eb36a26", + "test2.fasta_w_screen_hits.fna.gz:md5,8705f1efa7ce1551f054d9c403cf8433" ], [ [ - "test1.screen:md5,b074c6861bab21e2b3aa63aebff1f392", - "test2.screen:md5,b074c6861bab21e2b3aa63aebff1f392" + "test1.screen:md5,23d6d48a9488129b47ab89aa421b3be6", + "test2.screen:md5,23d6d48a9488129b47ab89aa421b3be6" ] ] ], @@ -33,16 +33,16 @@ [ [ [ - "all_samples_anicluster_representatives_virus.fna.gz:md5,07bf1a1918d0a5aa2422c7b1a3b1c085", - "all_samples_anicluster_representatives_virus_summary.tsv:md5,49535242cc88aebd1337c0d91e76e7f3" + "all_samples_anicluster_representatives_virus.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", + "all_samples_anicluster_representatives_virus_summary.tsv:md5,351e933fb6fb38a8e723f93723fbeffc" ], [ - "test1.fasta_w_screen_hits_virus.fna.gz:md5,3cc84b85ddcf944abd5a3a225b0ff404", - "test1.fasta_w_screen_hits_virus_summary.tsv:md5,791cd8249d24daf2dc3ea1f41aa3dba4" + "test1.fasta_w_screen_hits_virus.fna.gz:md5,1f2110292f923c979faf5b7086b850c5", + "test1.fasta_w_screen_hits_virus_summary.tsv:md5,351e933fb6fb38a8e723f93723fbeffc" ], [ - "test2.fasta_w_screen_hits_virus.fna.gz:md5,3221973668db26d28b3fcf3113d03b37", - "test2.fasta_w_screen_hits_virus_summary.tsv:md5,617215f2a883d4ec8d95aacd0b09d8a1" + "test2.fasta_w_screen_hits_virus.fna.gz:md5,30ef78b175e81c6bf26cb02472126faf", + "test2.fasta_w_screen_hits_virus_summary.tsv:md5,20375ce81322a9bd2a96a130e2c71101" ] ] ] @@ -52,51 +52,51 @@ [ [ "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,494ecf2153a3316d7f975bcc045b3cd7" + "viruses.fna.gz:md5,1e44a77c5e1ef9ae1f9004ba9e495548" ], [ "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,09b1e6883aac15f67d2f386661049166" + "viruses.fna.gz:md5,b386ca371a34b1870604771fe335b085" ] ] ], [ - "test1.filtered.fna.gz:md5,c5f61c2d487959d8b2bda90adde5a44a", - "test2.filtered.fna.gz:md5,741ab7b127375e64069553fa51b2eac9" + "test1.filtered.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", + "test2.filtered.fna.gz:md5,d8281f74354cc86bc9d42ef775220638" ] ], [ - "all_samples_anicluster_representatives.fna.gz:md5,07bf1a1918d0a5aa2422c7b1a3b1c085", + "all_samples_anicluster_representatives.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", [ - "all_samples_ani.tsv:md5,48b207f848d113168b6fb419d037731a" + "all_samples_ani.tsv:md5,a09126f3000f14bddf28c770ad9f92f7" ], [ - "all_samples_clusters.tsv:md5,1011f14e48fa1e74f68126345741cafb", + "all_samples_clusters.tsv:md5,06f4434bea86809af28ab16d91cb7b04", "versions.yml:md5,68070b01cdc8bf2e8ea2eb4b97d2cdad" ] ], "test1.bowtie2.log:md5,e7275c6347e7901c9bbb6ae4b317fcc1", [ [ - "all_samples_anicluster_representatives.fna.1.bt2:md5,2d27b4e32ccc71f6f7788dcef2aff18e", + "all_samples_anicluster_representatives.fna.1.bt2:md5,b27eb1ed0c9a3bedf4b3e2c6c107afcc", "all_samples_anicluster_representatives.fna.2.bt2:md5,ba6e4f623336917cb116c4632a6b0f82", "all_samples_anicluster_representatives.fna.3.bt2:md5,bc9a6e64bb55dfda29b4d8c18be153f1", "all_samples_anicluster_representatives.fna.4.bt2:md5,334c5e3e240a27fa3e942c891e1fc6c5", - "all_samples_anicluster_representatives.fna.rev.1.bt2:md5,c55ba4fc2275e2a5bc0638b55cdf2474", + "all_samples_anicluster_representatives.fna.rev.1.bt2:md5,32cf967b6670e1ba99e43c083dc2d425", "all_samples_anicluster_representatives.fna.rev.2.bt2:md5,dfd26c60bd10b1e376c9a0357576eb30" ] ], [ "Host_prediction_to_genus_m90.csv:md5,528dcefb6a6c743b43f0dbc40bec3692" ], - "test1.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", - "test2.IS_gene_info.tsv:md5,30955831e41455af9e653516ae6a9a6b", + "test1.IS_gene_info.tsv:md5,5eedecf429af2b560870e2203efa0f98", + "test2.IS_gene_info.tsv:md5,5eedecf429af2b560870e2203efa0f98", "software_versions.yml:md5,3d2ea4a6e456777a0a77bd88676f1994" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T14:13:15.109844835" + "timestamp": "2024-02-16T09:34:08.947794909" } -} +} \ No newline at end of file diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test b/workflows/phageannotator/tests/skip_genomad.nf.test index 2cea701..461e8eb 100644 --- a/workflows/phageannotator/tests/skip_genomad.nf.test +++ b/workflows/phageannotator/tests/skip_genomad.nf.test @@ -20,15 +20,17 @@ nextflow_workflow { """ } params { - outdir = "$outputDir" - skip_genomad = true - mash_screen_min_score = 0.5 - genomad_min_score = 0.01 - genomad_max_fdr = 1 - genomad_disable_nn = true - genomad_sensitivity = 0.1 - checkv_minimal_db = true - iphop_partial_test = true + outdir = "$outputDir" + skip_genomad = true + mash_screen_min_score = 1 + mash_screen_winner_take_all = true + genomad_min_score = 0.01 + genomad_max_fdr = 1 + genomad_disable_nn = true + genomad_sensitivity = 0.1 + checkv_minimal_db = true + checkv_min_length = 25000 + iphop_partial_test = true } } @@ -36,8 +38,8 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot(workflow.out).match() }, - { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 156 }, - { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 156 } + { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 9 }, + { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 9 } ) } } diff --git a/workflows/phageannotator/tests/skip_genomad.nf.test.snap b/workflows/phageannotator/tests/skip_genomad.nf.test.snap index de6b76d..a8b78e8 100644 --- a/workflows/phageannotator/tests/skip_genomad.nf.test.snap +++ b/workflows/phageannotator/tests/skip_genomad.nf.test.snap @@ -24,13 +24,13 @@ { "id": "test2" }, - "test2_quality_summary.tsv:md5,134567fa42775bd31cc4c59e9e3b1e95" + "test2_quality_summary.tsv:md5,943d161e6ea6cc7795c8454fe980c1c3" ], [ { "id": "test" }, - "test_quality_summary.tsv:md5,162b77bec682c86854b973563674ee01" + "test_quality_summary.tsv:md5,91f8c8ae4b4c62ce31ab3041dd2e0941" ] ], "3": [ @@ -38,13 +38,13 @@ { "id": "test2" }, - "test2.filtered.fna.gz:md5,3edfb732b7f8e340569a6be387493e3e" + "test2.filtered.fna.gz:md5,79206a59e5a337cbdf164e92000e52b2" ], [ { "id": "test" }, - "test.filtered.fna.gz:md5,05ad743c75dc1aea6884b7f4a0815b2e" + "test.filtered.fna.gz:md5,771bb2a2cdb8bd4468d158b4cae79db5" ] ], "4": [ @@ -52,7 +52,7 @@ { "id": "all_samples" }, - "all_samples_anicluster_representatives.fna.gz:md5,98e8ecda37d58a4527be87c6595d142d" + "all_samples_anicluster_representatives.fna.gz:md5,fcc8aed2c5786ef570a12d222345b34f" ] ], "5": [ @@ -68,7 +68,7 @@ { "id": "all_samples" }, - "all_samples_anicluster_representatives_taxonomy.tsv:md5,d75d2b561adf4f6fef576e27d564aefc" + "all_samples_anicluster_representatives_taxonomy.tsv:md5,c2cb503e207b7f0c1f8a69515d2604f3" ] ], "7": [ @@ -76,7 +76,7 @@ { "id": "all_samples" }, - "all_samples_cds_final_merged_output.tsv:md5,5f0e32592da6d396edf19d50ed9ba3ba" + "all_samples_cds_final_merged_output.tsv:md5,1315c8df1556d24b0e793e99e302196b" ] ], "8": [ @@ -84,13 +84,13 @@ { "id": "test2" }, - "test2.IS_gene_info.tsv:md5,e1090cd42f83f77a626325de8a3360e7" + "test2.IS_gene_info.tsv:md5,15ad6b92076f3c8f99075aed11bd7831" ], [ { "id": "test" }, - "test.IS_gene_info.tsv:md5,e1090cd42f83f77a626325de8a3360e7" + "test.IS_gene_info.tsv:md5,15ad6b92076f3c8f99075aed11bd7831" ] ], "9": [ @@ -139,7 +139,7 @@ { "id": "all_samples" }, - "all_samples_anicluster_representatives.fna.gz:md5,98e8ecda37d58a4527be87c6595d142d" + "all_samples_anicluster_representatives.fna.gz:md5,fcc8aed2c5786ef570a12d222345b34f" ] ], "filtered_viruses_fna_gz": [ @@ -147,13 +147,13 @@ { "id": "test2" }, - "test2.filtered.fna.gz:md5,3edfb732b7f8e340569a6be387493e3e" + "test2.filtered.fna.gz:md5,79206a59e5a337cbdf164e92000e52b2" ], [ { "id": "test" }, - "test.filtered.fna.gz:md5,05ad743c75dc1aea6884b7f4a0815b2e" + "test.filtered.fna.gz:md5,771bb2a2cdb8bd4468d158b4cae79db5" ] ], "host_predictions_tsv": [ @@ -169,13 +169,13 @@ { "id": "test2" }, - "test2.IS_gene_info.tsv:md5,e1090cd42f83f77a626325de8a3360e7" + "test2.IS_gene_info.tsv:md5,15ad6b92076f3c8f99075aed11bd7831" ], [ { "id": "test" }, - "test.IS_gene_info.tsv:md5,e1090cd42f83f77a626325de8a3360e7" + "test.IS_gene_info.tsv:md5,15ad6b92076f3c8f99075aed11bd7831" ] ], "marker_taxonomy_tsv": [ @@ -183,7 +183,7 @@ { "id": "all_samples" }, - "all_samples_anicluster_representatives_taxonomy.tsv:md5,d75d2b561adf4f6fef576e27d564aefc" + "all_samples_anicluster_representatives_taxonomy.tsv:md5,c2cb503e207b7f0c1f8a69515d2604f3" ] ], "pharokka_output_tsv": [ @@ -191,7 +191,7 @@ { "id": "all_samples" }, - "all_samples_cds_final_merged_output.tsv:md5,5f0e32592da6d396edf19d50ed9ba3ba" + "all_samples_cds_final_merged_output.tsv:md5,1315c8df1556d24b0e793e99e302196b" ] ], "versions": [ @@ -257,13 +257,13 @@ { "id": "test2" }, - "test2_quality_summary.tsv:md5,134567fa42775bd31cc4c59e9e3b1e95" + "test2_quality_summary.tsv:md5,943d161e6ea6cc7795c8454fe980c1c3" ], [ { "id": "test" }, - "test_quality_summary.tsv:md5,162b77bec682c86854b973563674ee01" + "test_quality_summary.tsv:md5,91f8c8ae4b4c62ce31ab3041dd2e0941" ] ] } @@ -272,6 +272,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-15T16:02:38.423761425" + "timestamp": "2024-02-16T09:06:50.306980862" } } \ No newline at end of file From 711f59a9beb99244d291676c4d729253a5bd49eb Mon Sep 17 00:00:00 2001 From: "Carson J. Miller" Date: Fri, 16 Feb 2024 12:54:00 -0800 Subject: [PATCH 23/23] Fixed pharokka snap --- .../tests/main.nf.test.snap | 6 +- tests/main.nf.test | 9 +-- tests/main.nf.test.snap | 58 +++++++++---------- 3 files changed, 37 insertions(+), 36 deletions(-) diff --git a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap index 007455c..676c73e 100644 --- a/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap +++ b/subworkflows/local/fasta_phage_function_pharokka/tests/main.nf.test.snap @@ -11,7 +11,7 @@ { "id": "test" }, - "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" + "test.gbk.gz:md5,8191d545d62d47bc90c73ba11f00f42d" ] ], "2": [ @@ -35,7 +35,7 @@ { "id": "test" }, - "test.gbk.gz:md5,6ac4cfdabe914505778956bc94bbed83" + "test.gbk.gz:md5,8191d545d62d47bc90c73ba11f00f42d" ] ], "versions": [ @@ -50,4 +50,4 @@ }, "timestamp": "2024-02-15T12:17:44.339900336" } -} \ No newline at end of file +} diff --git a/tests/main.nf.test b/tests/main.nf.test index f763093..83438a5 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -10,9 +10,10 @@ nextflow_pipeline { when { params { outdir = "$outputDir" + assembly_min_length = 3000 mash_screen_min_score = 1 mash_screen_winner_take_all = true - genomad_min_score = 0.01 + genomad_min_score = 0.7 genomad_max_fdr = 1 genomad_disable_nn = true genomad_sensitivity = 0.1 @@ -41,9 +42,9 @@ nextflow_pipeline { path("${params.outdir}/VirusMicrodiversity/instrain/profile/test2.IS/output/test2.IS_gene_info.tsv"), path("${params.outdir}/pipeline_info/software_versions.yml") ).match() }, - { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 4 }, - { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 4 }, - { assert path("${params.outdir}/VirusMicrodiversity/instrain/compare/all_samples.IS_compare/output/all_samples.IS_compare_pooled_SNV_data.tsv").readLines().size() == 15 }, + { assert path("${outputDir}/VirusLifestyle/bacphlip/all_samples_anicluster_representatives.fna.bacphlip").readLines().size() == 3 }, + { assert path("${outputDir}/VirusAbundance/coverm/contig/all_samples_alignment_results.tsv").readLines().size() == 3 }, + { assert path("${params.outdir}/VirusMicrodiversity/instrain/compare/all_samples.IS_compare/output/all_samples.IS_compare_pooled_SNV_data.tsv").readLines().size() == 11 }, { assert new File("$outputDir/ReadQuality/fastqc/test1_1_fastqc.html").exists() }, { assert new File("$outputDir/ReadQuality/fastqc/test1_2_fastqc.html").exists() }, { assert new File("$outputDir/VirusAbundance/bowtie2/align/test1.bam").exists() }, diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index 42a9cc8..7b744cb 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -12,20 +12,20 @@ [ [ [ - "test1.fasta.gz:md5,eb5b39fab473c61e4e73802d0e1ef518", - "test2.fasta.gz:md5,eb5b39fab473c61e4e73802d0e1ef518" + "test1.fasta.gz:md5,e47bee1d12b4f3ecc15357339a300685", + "test2.fasta.gz:md5,e47bee1d12b4f3ecc15357339a300685" ] ] ], [ [ - "test1.fasta_w_screen_hits.fna.gz:md5,8dff8263a5cc85fe5c816b208eb36a26", - "test2.fasta_w_screen_hits.fna.gz:md5,8705f1efa7ce1551f054d9c403cf8433" + "test1.fasta_w_screen_hits.fna.gz:md5,453c8afdaafa9fad8267808f018ff456", + "test2.fasta_w_screen_hits.fna.gz:md5,3b4c3ed1df7c4bba0d110d1848a46871" ], [ [ - "test1.screen:md5,23d6d48a9488129b47ab89aa421b3be6", - "test2.screen:md5,23d6d48a9488129b47ab89aa421b3be6" + "test1.screen:md5,813289ef6cc999555d271c334c90e02e", + "test2.screen:md5,813289ef6cc999555d271c334c90e02e" ] ] ], @@ -33,16 +33,16 @@ [ [ [ - "all_samples_anicluster_representatives_virus.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", - "all_samples_anicluster_representatives_virus_summary.tsv:md5,351e933fb6fb38a8e723f93723fbeffc" + "all_samples_anicluster_representatives_virus.fna.gz:md5,5e142dff15ca8215fa839315d1adcf2b", + "all_samples_anicluster_representatives_virus_summary.tsv:md5,24af1c4c95f590c93c2a765406777e20" ], [ - "test1.fasta_w_screen_hits_virus.fna.gz:md5,1f2110292f923c979faf5b7086b850c5", - "test1.fasta_w_screen_hits_virus_summary.tsv:md5,351e933fb6fb38a8e723f93723fbeffc" + "test1.fasta_w_screen_hits_virus.fna.gz:md5,e7673a3cd4d5f36f9068eea7060fd485", + "test1.fasta_w_screen_hits_virus_summary.tsv:md5,24af1c4c95f590c93c2a765406777e20" ], [ - "test2.fasta_w_screen_hits_virus.fna.gz:md5,30ef78b175e81c6bf26cb02472126faf", - "test2.fasta_w_screen_hits_virus_summary.tsv:md5,20375ce81322a9bd2a96a130e2c71101" + "test2.fasta_w_screen_hits_virus.fna.gz:md5,d7b52a92fd30684cf2af1f37b083dfd8", + "test2.fasta_w_screen_hits_virus_summary.tsv:md5,267cfcc8351ff339c0bcd7259eac652e" ] ] ] @@ -52,51 +52,51 @@ [ [ "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,1e44a77c5e1ef9ae1f9004ba9e495548" + "viruses.fna.gz:md5,fe58e669bc4af14ecbcb2182f5c7b7d2" ], [ "proviruses.fna.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "viruses.fna.gz:md5,b386ca371a34b1870604771fe335b085" + "viruses.fna.gz:md5,9b076877cee18dcfabf6ac5e513a198f" ] ] ], [ - "test1.filtered.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", - "test2.filtered.fna.gz:md5,d8281f74354cc86bc9d42ef775220638" + "test1.filtered.fna.gz:md5,5e142dff15ca8215fa839315d1adcf2b", + "test2.filtered.fna.gz:md5,42d3f558b541ab46aa1722a85fd47b96" ] ], [ - "all_samples_anicluster_representatives.fna.gz:md5,4ec0d3512efc98d941d3b334aa1ae6f1", + "all_samples_anicluster_representatives.fna.gz:md5,5e142dff15ca8215fa839315d1adcf2b", [ - "all_samples_ani.tsv:md5,a09126f3000f14bddf28c770ad9f92f7" + "all_samples_ani.tsv:md5,0e621266188df0cb908fcc6ad1486080" ], [ - "all_samples_clusters.tsv:md5,06f4434bea86809af28ab16d91cb7b04", + "all_samples_clusters.tsv:md5,eae06cf7ffafd72478bd943fbc5f516c", "versions.yml:md5,68070b01cdc8bf2e8ea2eb4b97d2cdad" ] ], - "test1.bowtie2.log:md5,e7275c6347e7901c9bbb6ae4b317fcc1", + "test1.bowtie2.log:md5,f161a0eae2eec7fcbfee0d7675d6ef0d", [ [ - "all_samples_anicluster_representatives.fna.1.bt2:md5,b27eb1ed0c9a3bedf4b3e2c6c107afcc", - "all_samples_anicluster_representatives.fna.2.bt2:md5,ba6e4f623336917cb116c4632a6b0f82", - "all_samples_anicluster_representatives.fna.3.bt2:md5,bc9a6e64bb55dfda29b4d8c18be153f1", - "all_samples_anicluster_representatives.fna.4.bt2:md5,334c5e3e240a27fa3e942c891e1fc6c5", - "all_samples_anicluster_representatives.fna.rev.1.bt2:md5,32cf967b6670e1ba99e43c083dc2d425", - "all_samples_anicluster_representatives.fna.rev.2.bt2:md5,dfd26c60bd10b1e376c9a0357576eb30" + "all_samples_anicluster_representatives.fna.1.bt2:md5,3140c35f6f861f1ccaf1833089c854c9", + "all_samples_anicluster_representatives.fna.2.bt2:md5,eeab4846bdfb11025cce1f0d89b0ab19", + "all_samples_anicluster_representatives.fna.3.bt2:md5,7dd079253884f7d2a1cb7b845b6e2bcc", + "all_samples_anicluster_representatives.fna.4.bt2:md5,482e19f50cd47fdde58bef83eacd0a3d", + "all_samples_anicluster_representatives.fna.rev.1.bt2:md5,f680250a61b5bbb90d7eba43b9ac3557", + "all_samples_anicluster_representatives.fna.rev.2.bt2:md5,3814fd4a34f1cf9f33bb684cd8fab198" ] ], [ "Host_prediction_to_genus_m90.csv:md5,528dcefb6a6c743b43f0dbc40bec3692" ], - "test1.IS_gene_info.tsv:md5,5eedecf429af2b560870e2203efa0f98", - "test2.IS_gene_info.tsv:md5,5eedecf429af2b560870e2203efa0f98", + "test1.IS_gene_info.tsv:md5,fa3090246663a1b4268f03f70fd04d72", + "test2.IS_gene_info.tsv:md5,fa3090246663a1b4268f03f70fd04d72", "software_versions.yml:md5,3d2ea4a6e456777a0a77bd88676f1994" ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-16T09:34:08.947794909" + "timestamp": "2024-02-16T12:46:20.921346103" } } \ No newline at end of file
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow