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added metrics as optional output

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This commit is contained in:
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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7
modules/gatk4/markduplicatesspark/main.nf
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@ -14,15 +14,16 @@ process GATK4_MARKDUPLICATES_SPARK {
path dict
output:
tuple val(meta), path("${prefix}"), emit: output
path "versions.yml" , emit: versions
tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.metrics"), emit: metrics, optional: true
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}" + ".bam"
def input_list = bam.collect{"--input $it"}.join(' ')