Merge pull request #1470 from maxulysse/multiqc_channels

Multiqc channels
nf-core · Apr 18, 2024 · 6b7a6b4 · 6b7a6b4
2 parents 0bf83b1 + 2a89fcc
commit 6b7a6b4
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Showing 3 changed files with 11 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -58,6 +58,7 @@ Balgattjåhkkå is the other top peak (over 2k m) in the Pårte massif, the othe
 - [#1462](https://github.com/nf-core/sarek/pull/1462) - Fix ascat input channels
 - [#1463](https://github.com/nf-core/sarek/pull/1463) - Add `spark` profile to all gatk4spark tests
 - [#1465](https://github.com/nf-core/sarek/pull/1465), [#1469](https://github.com/nf-core/sarek/pull/1469) - Fix input channels and tests of Sentieon workflows
+- [#1470](https://github.com/nf-core/sarek/pull/1470) - Fix channels for `MultiQC`
 
 ### Removed
 

diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf
@@ -41,7 +41,7 @@ workflow VCF_ANNOTATE_ALL {
     if (tools.split(',').contains('merge') || tools.split(',').contains('snpeff')) {
         VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache)
 
-        reports = reports.mix(VCF_ANNOTATE_SNPEFF.out.reports)
+        reports = reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ meta, reports -> [ reports ] })
         vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi)
         versions = versions.mix(VCF_ANNOTATE_SNPEFF.out.versions)
     }

diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
@@ -366,7 +366,7 @@ workflow SAREK {
             CRAM_QC_NO_MD(cram_skip_markduplicates, fasta, intervals_for_preprocessing)
 
             // Gather QC reports
-            reports = reports.mix(CRAM_QC_NO_MD.out.reports.collect{ meta, report -> report })
+            reports = reports.mix(CRAM_QC_NO_MD.out.reports.collect{ meta, report -> [ report ] })
 
             // Gather used softwares versions
             versions = versions.mix(CRAM_QC_NO_MD.out.versions)
@@ -380,7 +380,7 @@ workflow SAREK {
             cram_markduplicates_spark = BAM_MARKDUPLICATES_SPARK.out.cram
 
             // Gather QC reports
-            reports = reports.mix(BAM_MARKDUPLICATES_SPARK.out.reports.collect{ meta, report -> report })
+            reports = reports.mix(BAM_MARKDUPLICATES_SPARK.out.reports.collect{ meta, report -> [ report ] })
 
             // Gather used softwares versions
             versions = versions.mix(BAM_MARKDUPLICATES_SPARK.out.versions)
@@ -396,7 +396,7 @@ workflow SAREK {
             cram_sentieon_dedup = BAM_SENTIEON_DEDUP.out.cram
 
             // Gather QC reports
-            reports = reports.mix(BAM_SENTIEON_DEDUP.out.reports.collect{ meta, report -> report })
+            reports = reports.mix(BAM_SENTIEON_DEDUP.out.reports.collect{ meta, report -> [ report ] })
 
             // Gather used softwares versions
             versions = versions.mix(BAM_SENTIEON_DEDUP.out.versions)
@@ -410,7 +410,7 @@ workflow SAREK {
             cram_markduplicates_no_spark = BAM_MARKDUPLICATES.out.cram
 
             // Gather QC reports
-            reports = reports.mix(BAM_MARKDUPLICATES.out.reports.collect{ meta, report -> report })
+            reports = reports.mix(BAM_MARKDUPLICATES.out.reports.collect{ meta, report -> [ report ] })
 
             // Gather used softwares versions
             versions = versions.mix(BAM_MARKDUPLICATES.out.versions)
@@ -516,7 +516,7 @@ workflow SAREK {
                 ch_table_bqsr_no_spark,
                 ch_table_bqsr_spark)
 
-            reports = reports.mix(ch_table_bqsr.collect{ meta, table -> table })
+            reports = reports.mix(ch_table_bqsr.collect{ meta, table -> [ table ] })
 
             cram_applybqsr = ch_cram_for_bam_baserecalibrator.join(ch_table_bqsr, failOnDuplicate: true, failOnMismatch: true)
 
@@ -813,10 +813,10 @@ workflow SAREK {
         // QC
         VCF_QC_BCFTOOLS_VCFTOOLS(vcf_to_annotate, intervals_bed_combined)
 
-        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.bcftools_stats.collect{ meta, stats -> stats })
-        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect{ meta, counts -> counts })
-        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_qual.collect{ meta, qual -> qual })
-        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_filter_summary.collect{ meta, summary -> summary })
+        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.bcftools_stats.collect{ meta, stats -> [ stats ] })
+        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect{ meta, counts -> [ counts ] })
+        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_qual.collect{ meta, qual -> [ qual ] })
+        reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_filter_summary.collect{ meta, summary -> [ summary ] })
 
         CHANNEL_VARIANT_CALLING_CREATE_CSV(vcf_to_annotate, params.outdir)