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Multiqc channels #1470

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merged 3 commits into from
Apr 18, 2024
Merged

Multiqc channels #1470

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014b139
fix(multiqc-reports): fix the channel for multiqc reports
maxulysse Apr 18, 2024
8e850fd
fix(channels): fix remapping of channels
maxulysse Apr 18, 2024
2a89fcc
feat(CHANGELOG): update CHANGELOG
maxulysse Apr 18, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion subworkflows/local/vcf_annotate_all/main.nf
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Expand Up @@ -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)
}
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18 changes: 9 additions & 9 deletions workflows/sarek/main.nf
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Expand Up @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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)

Expand Down