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Sort TRGT merge inputs for stable outputs #9572

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Merged
fellen31 merged 1 commit into from
Dec 16, 2025
Merged

Sort TRGT merge inputs for stable outputs #9572

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3 changes: 2 additions & 1 deletion modules/nf-core/trgt/merge/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ process TRGT_MERGE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input = (vcfs.collect().size() > 1) ? vcfs.sort{ vcf -> vcf.name } : vcfs
def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
Expand All @@ -37,7 +38,7 @@ process TRGT_MERGE {
$args \\
$reference \\
$output \\
--vcf ${vcfs}
--vcf ${input}
"""

stub:
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