Skip to content
Snippets Groups Projects
Commit 47737412 authored by ffinfo's avatar ffinfo
Browse files

Fixed empty readgroup arg

parent 000b9fac
No related branches found
No related tags found
1 merge request!57Fixed defaults
......@@ -39,12 +39,14 @@ task Mem {
String picardCommand = if (defined(bwaIndex.altIndex)) then sortSamCommand + " | " + setNmMdAndUqTagsCommand
else sortSamCommand
String readgroupArg = if (defined(readgroup)) then "-R '" + readgroup + "'" else ""
command {
set -e -o pipefail
mkdir -p $(dirname ~{outputPath})
~{preCommand}
bwa mem ~{"-t " + threads} \
~{"-R '" + readgroup + "'"} \
~{readgroupArg} \
~{bwaIndex.fastaFile} \
~{inputR1} \
~{inputR2} \
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment