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remove unnecessary if statement

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This commit is contained in:
SusiJo 2022-05-20 13:25:57 +02:00
parent 153c900d0e
commit bdf222649d
1 changed files with 3 additions and 9 deletions
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12
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, cnvkit runs natively on bam but is prohibitively slow // 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}"
@ -35,7 +35,8 @@ process CNVKIT_BATCH {
def normal_exists = normal ? true: false def normal_exists = normal ? true: false
// tumor_only mode does not need fasta & target // tumor_only mode does not need fasta & target
// instead it requires a pre-computed reference.cnn which is built from fasta & target // instead it requires a pre-computed reference.cnn which is built from fasta & target
def (normal_out, normal_args, fasta_args, target_args) = ["", "", "", ""] def (normal_out, normal_args, fasta_args) = ["", "", ""]
def target_args = targets ? "--targets $targets" : ""
def reference_args = reference ? "--reference $reference" : "" def reference_args = reference ? "--reference $reference" : ""
if (normal_exists){ if (normal_exists){
@ -45,13 +46,6 @@ process CNVKIT_BATCH {
fasta_args = fasta ? "--fasta $fasta" : "" fasta_args = fasta ? "--fasta $fasta" : ""
} }
if (args.contains("--method wgs") || args.contains("-m wgs")) {
target_args = targets ? "--targets $targets" : ""
}
else {
target_args = "--targets $targets"
}
""" """
if $is_cram; then if $is_cram; then
samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out