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[refs #119] Adds Control-FREEC output
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mark-welsh committed Sep 24, 2019
1 parent 3311a15 commit e46574c
Showing 1 changed file with 8 additions and 1 deletion.
9 changes: 8 additions & 1 deletion control-freec/control-freec.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,10 @@ task ControlFREEC {
Int cpu = 4
}

Int pymem = round(memory)
String copynumber_filename = basename(tumor_input, ".bam") + ".bam_sample.cpn"
String ratio_filename = basename(tumor_input, ".bam") + ".bam_ratio.txt"
String cnv_filename = basename(tumor_input, ".bam") + ".bam_CNVS"
String bam_info_filename = basename(tumor_input, ".bam") + ".bam_info.txt"

command <<<
set -Eeuxo pipefail;
Expand Down Expand Up @@ -81,6 +84,10 @@ task ControlFREEC {
>>>

output {
File copynumber_file = "~{copynumber_filename}"
File ratio_file = "~{ratio_filename}"
File cnv_file = "~{cnv_filename}"
File bam_info_file = "~{bam_info_filename}"
}

runtime {
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