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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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SusiJo 2022-05-20 13:08:26 +02:00 committed by GitHub
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commit 2e5aa0dbb4
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modules/cnvkit/batch/main.nf
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@ -31,7 +31,7 @@ process CNVKIT_BATCH {
// input pair is assumed to have same extension if both exist
def is_cram = tumor.Extension == "cram" ? true : false
def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
// do not run samtools on normal samples in tumor_only
// do not run samtools on normal samples in tumor_only mode
def normal_exists = normal ? true: false
// tumor_only mode does not need fasta & target
// instead it requires a pre-computed reference which is built from fasta & target