millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

remove unnecessary if statement

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

10
modules/cnvkit/batch/main.nf
View file

@ -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