From e46574cd5f6614b35899591bfb92c33794785dfb Mon Sep 17 00:00:00 2001 From: Mark Welsh Date: Tue, 24 Sep 2019 15:52:08 -0400 Subject: [PATCH] [refs #119] Adds Control-FREEC output --- control-freec/control-freec.wdl | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/control-freec/control-freec.wdl b/control-freec/control-freec.wdl index f7eb908..82cfda5 100644 --- a/control-freec/control-freec.wdl +++ b/control-freec/control-freec.wdl @@ -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; @@ -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 {