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fix(markduplicates): avoid duplicate alignment emission under -stub #2277

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fix(markduplicates): avoid duplicate alignment emission under -stub #2277

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830f740
fix(markduplicates): avoid duplicate alignment emission under -stub
gburnett-nvidia Aug 25, 2026
db3e153
fix: removing reference to params inside subworkflow, replaced with take
gburnett-nvidia Aug 25, 2026
71e747c
chore: update changelog
gburnett-nvidia Aug 26, 2026
523eddc
Merge branch 'dev' into fix-markduplicates-stub-duplicate
gburnett-nvidia Aug 26, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
#### Fixed

- [#2268](https://github.com/nf-core/sarek/pull/2268) - Resolve filetype output for parabricks/fq2bam
- [#2277](https://github.com/nf-core/sarek/pull/2277) - fix(markduplicates): avoid duplicate alignment emission under -stub

#### Removed

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13 changes: 8 additions & 5 deletions subworkflows/local/bam_markduplicates/main.nf
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Expand Up @@ -13,6 +13,7 @@ workflow BAM_MARKDUPLICATES {
fasta // channel: [mandatory] [ fasta ]
fasta_fai // channel: [mandatory] [ fasta_fai ]
intervals_bed_combined // channel: [optional] [ intervals_bed ]
save_output_as_bam // boolean: [mandatory] true = emit bam, false = emit cram

main:
reports = channel.empty()
Expand All @@ -22,11 +23,13 @@ workflow BAM_MARKDUPLICATES {
// module emits .bai inline; CRAM mode emits .crai via samtools post-conversion.
GATK4_MARKDUPLICATES(bam, fasta.map{ _meta, fasta_ -> [ fasta_ ] }, fasta_fai.map{ _meta, fasta_fai_ -> [ fasta_fai_ ] })

// Unified alignment output — BAM or CRAM depending on save_output_as_bam
alignment = GATK4_MARKDUPLICATES.out.bam
.join(GATK4_MARKDUPLICATES.out.bai, failOnDuplicate: true, failOnMismatch: true)
.mix(GATK4_MARKDUPLICATES.out.cram
.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true))
// Unified alignment output — BAM or CRAM depending on save_output_as_bam.
// Select explicitly rather than mixing both optional channels together: the module's stub
// block touches both bam and cram outputs unconditionally, so relying on "only one is ever
// populated" doubles every downstream emission under -stub.
alignment = save_output_as_bam
? GATK4_MARKDUPLICATES.out.bam.join(GATK4_MARKDUPLICATES.out.bai, failOnDuplicate: true, failOnMismatch: true)
: GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true)

// QC on alignment
CRAM_QC_MOSDEPTH_SAMTOOLS(alignment, fasta, fasta_fai, intervals_bed_combined)
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3 changes: 2 additions & 1 deletion subworkflows/local/fastq_preprocess_gatk/main.nf
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Expand Up @@ -313,7 +313,8 @@ workflow FASTQ_PREPROCESS_GATK {
cram_for_markduplicates,
fasta,
fasta_fai,
intervals_for_preprocessing)
intervals_for_preprocessing,
params.save_output_as_bam)

cram_markduplicates_no_spark = BAM_MARKDUPLICATES.out.alignment

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