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add output default bam

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This commit is contained in:
Rike 2022-05-12 18:06:15 +02:00
parent 3fda3903dc
commit 99880654bf
2 changed files with 1 additions and 2 deletions
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2
modules/gatk4/markduplicatesspark/main.nf
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@ -22,7 +22,7 @@ process GATK4_MARKDUPLICATES_SPARK {
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}.bam"
def input_list = bam.collect{"--input $it"}.join(' ')
def avail_mem = 3

1
tests/modules/gatk4/markduplicatesspark/nextflow.config
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@ -1,5 +1,4 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}