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POC: declare ext variable defaults as directives #8808

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7de971b
poc with samtools/sort
nvnieuwk Jul 24, 2025
311bd0a
use smoove as another example
nvnieuwk Jul 24, 2025
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12 changes: 6 additions & 6 deletions modules/nf-core/samtools/sort/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
process SAMTOOLS_SORT {
tag "$meta.id"
label 'process_medium'
ext prefix: "${meta.id}", args: '', when: true

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
Expand All @@ -18,12 +19,11 @@ process SAMTOOLS_SORT {
tuple val(meta), path("*.csi"), emit: csi, optional: true
path "versions.yml", emit: versions

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args
def prefix = task.ext.prefix
def extension = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt cram") ? "cram" :
"bam"
Expand All @@ -49,8 +49,8 @@ process SAMTOOLS_SORT {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args
def prefix = task.ext.prefix
def extension = args.contains("--output-fmt sam") ? "sam" :
args.contains("--output-fmt cram") ? "cram" :
"bam"
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10 changes: 5 additions & 5 deletions modules/nf-core/smoove/call/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
process SMOOVE_CALL {
tag "$meta.id"
label 'process_high'
ext prefix: "${meta.id}", args: '', when: true

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
Expand All @@ -16,12 +17,11 @@ process SMOOVE_CALL {
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions

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

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args
def prefix = task.ext.prefix

def exclude = exclude_beds ? "--exclude ${exclude_beds}" : ""
"""
Expand All @@ -41,7 +41,7 @@ process SMOOVE_CALL {
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix
"""
echo "" | gzip > ${prefix}.vcf.gz

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