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split the fastq and fastq_idx outputs from cellranger mkfastq module #8673

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split the fastq and fastq_idx outputs from cellranger mkfastq module #8673

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34dfb53
split the fastq and fastq_idx outputs from cellranger mkfastq module
gordond88 Jun 19, 2025
0fb38a5
output path bugfix
gordond88 Jun 19, 2025
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13 changes: 7 additions & 6 deletions modules/nf-core/cellranger/mkfastq/main.nf
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Original file line number Diff line number Diff line change
@@ -8,12 +8,13 @@ process CELLRANGER_MKFASTQ {
tuple val(meta), path(csv), path(bcl)

output:
tuple val(meta), path("*_outs/outs/fastq_path/**/*.fastq.gz") , emit: fastq
tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq
tuple val(meta), path("*_outs/outs/fastq_path/Reports") , optional:true, emit: reports
tuple val(meta), path("*_outs/outs/fastq_path/Stats") , optional:true, emit: stats
tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop
path "versions.yml" , emit: versions
tuple val(meta), path("*_outs/outs/fastq_path/**/**_S[1-9]*_R?_00?.fastq.gz") , emit: fastq
tuple val(meta), path("*_outs/outs/fastq_path/**/**_S[1-9]*_I?_00?.fastq.gz") , optional:true, emit: fastq_idx
tuple val(meta), path("*_outs/outs/fastq_path/Undetermined*.fastq.gz") , optional:true, emit: undetermined_fastq
tuple val(meta), path("*_outs/outs/fastq_path/Reports") , optional:true, emit: reports
tuple val(meta), path("*_outs/outs/fastq_path/Stats") , optional:true, emit: stats
tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when