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added metrics as optional output

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SusiJo 2022-05-31 14:34:50 +02:00
parent b34e5ea6bf
commit 39e34418c9
1 changed files with 4 additions and 3 deletions
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modules/gatk4/markduplicatesspark/main.nf
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@ -14,7 +14,8 @@ process GATK4_MARKDUPLICATES_SPARK {
path dict
output:
tuple val(meta), path("${prefix}"), emit: output
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.metrics"), emit: metrics, optional: true
path "versions.yml" , emit: versions
when:
@ -22,7 +23,7 @@ process GATK4_MARKDUPLICATES_SPARK {
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}" + ".bam"
def input_list = bam.collect{"--input $it"}.join(' ')