Merge pull request #247 from danilodileo/review-more-updates

changes
nf-core · Jan 24, 2024 · 45881d3 · 45881d3
2 parents 05cc258 + f04fe3d
commit 45881d3
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Showing 4 changed files with 14 additions and 12 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,7 +42,7 @@ jobs:
   profiles:
     name: Run workflow profile
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metadenovo') }}
+    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metatdenovo') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:

diff --git a/modules/local/eggnog/mapper.nf b/modules/local/eggnog/mapper.nf
@@ -27,7 +27,7 @@ process EGGNOG_MAPPER {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-    input    = fasta =~ /\.gz$/ ? fasta.name.take(fasta.name.lastIndexOf('.')) : fasta
+    input    = fasta.name.endsWith(".gz") ? fasta.baseName : fasta
     gunzip   = fasta =~ /\.gz$/ ? "gunzip -c ${fasta} > ${input}" : ""
 
     """

diff --git a/subworkflows/local/eukulele.nf b/subworkflows/local/eukulele.nf
@@ -19,13 +19,15 @@ workflow SUB_EUKULELE {
     ch_versions = ch_versions.mix ( EUKULELE_SEARCH.out.versions )
 
     FORMAT_TAX( EUKULELE_SEARCH.out.taxonomy_estimation.map { [ it[0], it[1] ] } )
+    ch_versions = ch_versions.mix ( FORMAT_TAX.out.versions )
 
     FORMAT_TAX.out.tax
         .join(eukulele)
         .map { [ it[0], it[3], it[1] ] }
         .set { ch_sum_taxonomy }
 
     SUM_TAXONOMY ( ch_sum_taxonomy, feature_counts )
+    ch_versions = ch_versions.mix ( SUM_TAXONOMY.out.versions )
 
     emit:
     taxonomy_summary    = SUM_TAXONOMY.out.taxonomy_summary

diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf
@@ -29,9 +29,9 @@ if ( params.assembly ) {
 if ( params.gff && params.protein_fasta ) {
     orf_caller = 'user_orfs'
 } else if ( params.gff && ! params.protein_fasta ) {
-    exit 1, 'When supplying ORFs, both --gff and --protein_fasta must be specified, --protein_fasta file is missing!'
+    error 'When supplying ORFs, both --gff and --protein_fasta must be specified, --protein_fasta file is missing!'
 } else if ( params.protein_fasta && ! params.gff ) {
-    exit 1, 'When supplying ORFs, both --gff and --protein_fasta must be specified, --gff file is missing!'
+    error 'When supplying ORFs, both --gff and --protein_fasta must be specified, --gff file is missing!'
 } else {
     orf_caller = params.orf_caller
 }
@@ -173,7 +173,7 @@ workflow METATDENOVO {
     .mix(ch_fastq.single)
     .set { ch_cat_fastq }
 
-    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first())
 
     //
     // SUBWORKFLOW: Read QC and trim adapters
@@ -215,7 +215,7 @@ workflow METATDENOVO {
         ch_collect_stats
             .combine(ch_bbduk_logs)
             .set {ch_collect_stats}
-        ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBDUK.out.log.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(BBMAP_BBDUK.out.log.collect{it[1]})
     } else {
         ch_clean_reads  = FASTQC_TRIMGALORE.out.reads
         ch_bbduk_logs = Channel.empty()
@@ -302,7 +302,7 @@ workflow METATDENOVO {
             .map { [ [ id: 'megahit' ], it ] }
             .set { ch_assembly_contigs }
         ch_versions = ch_versions.mix(MEGAHIT_INTERLEAVED.out.versions)
-    } else { exit 1, 'Assembler not specified!' }
+    } else { error 'Assembler not specified!' }
 
     // If the user asked for length filtering, perform that with SEQTK_SEQ (the actual length parameter is used in modules.config)
     if ( params.min_contig_length > 0 ) {
@@ -325,7 +325,7 @@ workflow METATDENOVO {
         ch_versions      = ch_versions.mix(PROKKA_SUBSETS.out.versions)
         ch_gff           = UNPIGZ_GFF.out.unzipped
         ch_protein       = PROKKA_SUBSETS.out.faa
-        ch_multiqc_files = ch_multiqc_files.mix(PROKKA_SUBSETS.out.prokka_log.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(PROKKA_SUBSETS.out.prokka_log.collect{it[1]})
      }
 
     //
@@ -522,10 +522,10 @@ workflow METATDENOVO {
     ch_methods_description = Channel.value(methods_description)
 
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(TRANSRATE.out.assembly_qc.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(BAM_SORT_STATS_SAMTOOLS.out.idxstats.collect{it[1]}.ifEmpty([]))
-    ch_multiqc_files = ch_multiqc_files.mix(FEATURECOUNTS_CDS.out.summary.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(TRANSRATE.out.assembly_qc.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(BAM_SORT_STATS_SAMTOOLS.out.idxstats.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(FEATURECOUNTS_CDS.out.summary.collect{it[1]})
 
 
     MULTIQC (