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Use mode copy in publishDir [CW-7279]

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This commit is contained in:
Natalia Garcia 2026-05-27 09:29:30 +00:00
parent dda764f48c
commit 7e301319fc
1 changed files with 3 additions and 3 deletions
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6
subworkflows/mods.nf
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@ -44,7 +44,7 @@ process runModkitPileup {
tuple val(alias), tuple val(alias),
path("${alias}.mods.bedmethyl.gz"), path("${alias}.mods.bedmethyl.gz"),
emit: bedmethyl emit: bedmethyl
publishDir "${params.out_dir}/${output_key}/mods" publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
script: script:
output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef
@ -77,7 +77,7 @@ process modkit_tobigwig {
tuple val(alias), tuple val(alias),
path("${alias}.mods.*.bw"), path("${alias}.mods.*.bw"),
emit: bigwig emit: bigwig
publishDir "${params.out_dir}/${output_key}/mods" publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
script: script:
output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef
@ -112,7 +112,7 @@ process summariseModkitBedmethyl {
tuple val(alias), tuple val(alias),
path("${alias}.mods.summary.tsv"), path("${alias}.mods.summary.tsv"),
emit: summary emit: summary
publishDir "${params.out_dir}/${output_key}/mods" publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
script: script:
output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef output_key = alias == "cohort" ? "cohort" : "samples/${alias}" // nodef