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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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SusiJo 2022-05-20 13:07:57 +02:00 committed by GitHub
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modules/cnvkit/batch/main.nf
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@ -27,7 +27,7 @@ process CNVKIT_BATCH {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
// execute samtools only when cram files are input // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
// input pair is assumed to have same extension if both exist // input pair is assumed to have same extension if both exist
def is_cram = tumor.Extension == "cram" ? true : false def is_cram = tumor.Extension == "cram" ? true : false
def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}" def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"