From aa25a441a70adf2d9dd567951745964de37dde8e Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 16 Jan 2024 17:41:58 +0100 Subject: [PATCH 1/7] input_fasta channel fixed --- workflows/metatdenovo.nf | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index 00d3e17d..58aa8ccc 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -325,7 +325,7 @@ workflow METATDENOVO { // Call ORFs // ch_gff = Channel.empty() - ch_aa = Channel.empty() + ch_protein = Channel.empty() if ( ! params.protein_fasta & ! params.gff ) { @@ -337,7 +337,7 @@ workflow METATDENOVO { UNPIGZ_GFF(PROKKA_SUBSETS.out.gff.map { [ [id: "${params.orf_caller}.${it[0].id}"], it[1] ] }) ch_versions = ch_versions.mix(PROKKA_SUBSETS.out.versions) ch_gff = UNPIGZ_GFF.out.unzipped - ch_aa = PROKKA_SUBSETS.out.faa + ch_protein = PROKKA_SUBSETS.out.faa ch_multiqc_files = ch_multiqc_files.mix(PROKKA_SUBSETS.out.prokka_log.collect{it[1]}.ifEmpty([])) } @@ -348,7 +348,7 @@ workflow METATDENOVO { PRODIGAL( ch_assembly_contigs.map { [ [id: "${params.assembler}.${params.orf_caller}"], it[1] ] } ) UNPIGZ_GFF(PRODIGAL.out.gff.map { [ [id: "${it[0].id}.${params.orf_caller}"], it[1] ] }) ch_gff = UNPIGZ_GFF.out.unzipped - ch_aa = PRODIGAL.out.faa + ch_protein = PRODIGAL.out.faa ch_versions = ch_versions.mix(PRODIGAL.out.versions) } @@ -358,7 +358,7 @@ workflow METATDENOVO { if ( params.orf_caller == 'transdecoder' ) { TRANSDECODER ( ch_assembly_contigs.map { [ [id: "transdecoder.${it[0].id}" ], it[1] ] } ) ch_gff = TRANSDECODER.out.gff - ch_aa = TRANSDECODER.out.pep + ch_protein = TRANSDECODER.out.pep ch_versions = ch_versions.mix(TRANSDECODER.out.versions) } } else if ( ! params.protein_fasta ) { @@ -390,7 +390,7 @@ workflow METATDENOVO { // SUBWORKFLOW: classify ORFs with a set of hmm files // ch_hmmrs - .combine(ch_aa) + .combine(ch_protein) .map { [ [ id: "${params.assembler}.${params.orf_caller}" ], it[0], it[2] ] } .set { ch_hmmclassify } HMMCLASSIFY ( ch_hmmclassify ) @@ -436,11 +436,11 @@ workflow METATDENOVO { if ( ! params.skip_eggnog ) { File directory = new File(params.eggnog_dbpath) if ( ! directory.exists() ) { directory.mkdir() } - EGGNOG(params.eggnog_dbpath, ch_aa, ch_fcs_for_summary ) + EGGNOG(params.eggnog_dbpath, ch_protein, ch_fcs_for_summary ) ch_versions = ch_versions.mix(EGGNOG.out.versions) ch_merge_tables = EGGNOG.out.sumtable } else { - ch_aa + ch_protein .map { [ it[0], [] ] } .set { ch_merge_tables } } @@ -450,7 +450,7 @@ workflow METATDENOVO { // SUBWORKFLOW: run kofamscan on the ORF-called amino acid sequences // if( !params.skip_kofamscan ) { - ch_aa + ch_protein .map { [ it[0], it[1] ] } .set { ch_kofamscan } KOFAMSCAN( ch_kofamscan, params.kofam_dir, ch_fcs_for_summary) @@ -506,7 +506,7 @@ workflow METATDENOVO { File directory = new File(params.eukulele_dbpath) if ( ! directory.exists() ) { directory.mkdir() } ch_directory = Channel.fromPath( directory ) - ch_aa + ch_protein .map {[ [ id:"${it[0].id}" ], it[1] ] } .combine( ch_eukulele_db ) .set { ch_eukulele } From 3e3d24ee955a5ead1ad7961ef98b4c9f35341d24 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Tue, 16 Jan 2024 17:50:13 +0100 Subject: [PATCH 2/7] Update workflows/metatdenovo.nf Co-authored-by: Daniel Lundin --- workflows/metatdenovo.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index 65f06d08..93e315c5 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -324,7 +324,7 @@ workflow METATDENOVO { // // Call ORFs // - ch_gff = Channel.empty() + ch_gff = Channel.empty() ch_protein = Channel.empty() if ( ! params.protein_fasta & ! params.gff ) { From d40637550e44aca6b856fcad6e51514430189f4b Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Tue, 16 Jan 2024 17:50:23 +0100 Subject: [PATCH 3/7] Update workflows/metatdenovo.nf Co-authored-by: Daniel Lundin --- workflows/metatdenovo.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index 93e315c5..aaec597a 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -337,7 +337,7 @@ workflow METATDENOVO { UNPIGZ_GFF(PROKKA_SUBSETS.out.gff.map { [ [id: "${params.orf_caller}.${it[0].id}"], it[1] ] }) ch_versions = ch_versions.mix(PROKKA_SUBSETS.out.versions) ch_gff = UNPIGZ_GFF.out.unzipped - ch_protein = PROKKA_SUBSETS.out.faa + ch_protein = PROKKA_SUBSETS.out.faa ch_multiqc_files = ch_multiqc_files.mix(PROKKA_SUBSETS.out.prokka_log.collect{it[1]}.ifEmpty([])) } From f72ba60d564cb50940e80e850779dd34c3e45884 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Tue, 16 Jan 2024 17:50:30 +0100 Subject: [PATCH 4/7] Update workflows/metatdenovo.nf Co-authored-by: Daniel Lundin --- workflows/metatdenovo.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index aaec597a..9a7affc2 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -348,7 +348,7 @@ workflow METATDENOVO { PRODIGAL( ch_assembly_contigs.map { [ [id: "${params.assembler}.${params.orf_caller}"], it[1] ] } ) UNPIGZ_GFF(PRODIGAL.out.gff.map { [ [id: "${it[0].id}.${params.orf_caller}"], it[1] ] }) ch_gff = UNPIGZ_GFF.out.unzipped - ch_protein = PRODIGAL.out.faa + ch_protein = PRODIGAL.out.faa ch_versions = ch_versions.mix(PRODIGAL.out.versions) } From 4373ad8479a424b636b003c6d3223e7167bbed92 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Tue, 16 Jan 2024 17:50:35 +0100 Subject: [PATCH 5/7] Update workflows/metatdenovo.nf Co-authored-by: Daniel Lundin --- workflows/metatdenovo.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index 9a7affc2..1d26b638 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -358,7 +358,7 @@ workflow METATDENOVO { if ( params.orf_caller == 'transdecoder' ) { TRANSDECODER ( ch_assembly_contigs.map { [ [id: "transdecoder.${it[0].id}" ], it[1] ] } ) ch_gff = TRANSDECODER.out.gff - ch_protein = TRANSDECODER.out.pep + ch_protein = TRANSDECODER.out.pep ch_versions = ch_versions.mix(TRANSDECODER.out.versions) } } else if ( ! params.protein_fasta ) { From b5fda3792b21fcfc0d35b35b86fd52e6f7537198 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 16 Jan 2024 17:51:07 +0100 Subject: [PATCH 6/7] lint --- modules.json | 106 ++++++++++++++++++++++++++++++++++++++------------- 1 file changed, 79 insertions(+), 27 deletions(-) diff --git a/modules.json b/modules.json index f3764eb3..41f49010 100644 --- a/modules.json +++ b/modules.json @@ -8,122 +8,170 @@ "bbmap/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "617777a807a1770f73deb38c80004bac06807eef", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "prodigal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "prokka": { "branch": "master", "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/sort": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/stats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "seqtk/mergepe": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "subread/featurecounts": { "branch": "master", "git_sha": "d062b356938ea98d29b298691adf0620d3c3bdf0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "transdecoder/longorf": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "transdecoder/predict": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -132,15 +180,19 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] } } } } } -} +} \ No newline at end of file From d08f0832dd44549955e6502f9483e857f809d721 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 16 Jan 2024 17:51:28 +0100 Subject: [PATCH 7/7] prettier --- modules.json | 106 +++++++++++++-------------------------------------- 1 file changed, 27 insertions(+), 79 deletions(-) diff --git a/modules.json b/modules.json index 41f49010..f3764eb3 100644 --- a/modules.json +++ b/modules.json @@ -8,170 +8,122 @@ "bbmap/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "617777a807a1770f73deb38c80004bac06807eef", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prodigal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prokka": { "branch": "master", "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/sort": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "seqtk/mergepe": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "d062b356938ea98d29b298691adf0620d3c3bdf0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/longorf": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/predict": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -180,19 +132,15 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] } } } } } -} \ No newline at end of file +}