From 014b139686676011d6d27f06525ee0e40f71044f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 18 Apr 2024 09:48:31 +0200 Subject: [PATCH 1/3] fix(multiqc-reports): fix the channel for multiqc reports --- workflows/sarek/main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index 1152ed857b..212fe383a2 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -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) @@ -851,7 +851,7 @@ workflow SAREK { // Gather used softwares versions versions = versions.mix(VCF_ANNOTATE_ALL.out.versions) - reports = reports.mix(VCF_ANNOTATE_ALL.out.reports) + reports = reports.mix(VCF_ANNOTATE_ALL.out.reports.collect{ meta, reports -> [ reports ] }) } } From 8e850fdcf261702ab36f4ccd8ae5fbf7ee129e6a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 18 Apr 2024 09:56:41 +0200 Subject: [PATCH 2/3] fix(channels): fix remapping of channels --- subworkflows/local/vcf_annotate_all/main.nf | 2 +- workflows/sarek/main.nf | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index 89d4b696c3..20cab4be1c 100644 --- 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 index 212fe383a2..5062470373 100644 --- 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) @@ -851,7 +851,7 @@ workflow SAREK { // Gather used softwares versions versions = versions.mix(VCF_ANNOTATE_ALL.out.versions) - reports = reports.mix(VCF_ANNOTATE_ALL.out.reports.collect{ meta, reports -> [ reports ] }) + reports = reports.mix(VCF_ANNOTATE_ALL.out.reports) } } From 2a89fcc1fc442dadaac7b91a0a5509adcc4b5709 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 18 Apr 2024 09:58:46 +0200 Subject: [PATCH 3/3] feat(CHANGELOG): update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index be4e30c5a6..5d33748b43 100644 --- 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