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feat: nicer syntax (#1286)

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* feat: nicer syntax

* feat: code polishing

* feat: code polishing
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Maxime U. Garcia 2022-02-11 16:07:52 +01:00 committed by GitHub
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modules/manta/germline/main.nf
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@ -29,10 +29,11 @@ process MANTA_GERMLINE {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_files = input.collect{"--bam ${it}"}.join(' ')
def options_manta = target_bed ? "--callRegions $target_bed" : "" def options_manta = target_bed ? "--callRegions $target_bed" : ""
""" """
configManta.py \ configManta.py \
--bam ${input.join(' --bam ')} \ ${input_files} \
--reference $fasta \ --reference $fasta \
--runDir manta \ --runDir manta \
$options_manta \ $options_manta \