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improve readability

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This commit is contained in:
SusiJo 2022-05-20 13:29:49 +02:00
parent bdf222649d
commit 9096be5464
1 changed files with 5 additions and 2 deletions
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7
modules/cnvkit/batch/main.nf
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@ -27,17 +27,17 @@ process CNVKIT_BATCH {
script:
def args = task.ext.args ?: ''
// 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
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 mode
def normal_exists = normal ? true: false
// tumor_only mode does not need fasta & target
// instead it requires a pre-computed reference.cnn which is built from fasta & target
def (normal_out, normal_args, fasta_args) = ["", "", ""]
def target_args = targets ? "--targets $targets" : ""
def reference_args = reference ? "--reference $reference" : ""
if (normal_exists){
def normal_prefix = normal.BaseName
@ -46,6 +46,9 @@ process CNVKIT_BATCH {
fasta_args = fasta ? "--fasta $fasta" : ""
}
def target_args = targets ? "--targets $targets" : ""
def reference_args = reference ? "--reference $reference" : ""
"""
if $is_cram; then
samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out