From d8d8af25ec15bb5a13ce0d5b4631a69f8a079a52 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 2 Jul 2019 15:36:18 +0200
Subject: [PATCH] address strelka and manta changes
---
manta.wdl | 4 +---
strelka.wdl | 8 ++------
2 files changed, 3 insertions(+), 9 deletions(-)
diff --git a/manta.wdl b/manta.wdl
index 546d468..f2e1d43 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -10,7 +10,7 @@ task Somatic {
File? normalBamIndex
File referenceFasta
File referenceFastaFai
- String runDir = "."
+ String runDir = "./manta_run"
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -22,8 +22,6 @@ task Somatic {
}
command {
- mkdir -p ~{runDir}
- set -e
configManta.py \
~{"--normalBam " + normalBam} \
~{"--tumorBam " + tumorBam} \
diff --git a/strelka.wdl b/strelka.wdl
index 262d3fd..f5cd525 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -4,7 +4,7 @@ import "common.wdl" as common
task Germline {
input {
- String runDir = "."
+ String runDir = "./strelka_run"
Array[File]+ bams
Array[File]+ indexes
File referenceFasta
@@ -20,8 +20,6 @@ task Germline {
}
command {
- set -e
- mkdir -p ~{runDir}
configureStrelkaGermlineWorkflow.py \
--bam ~{sep=" --bam " bams} \
--ref ~{referenceFasta} \
@@ -50,7 +48,7 @@ task Germline {
task Somatic {
input {
- String runDir = "."
+ String runDir = "./strelka_run"
File normalBam
File normalBamIndex
File tumorBam
@@ -71,8 +69,6 @@ task Somatic {
}
command {
- set -e
- mkdir -p ~{runDir}
configureStrelkaSomaticWorkflow.py \
--normalBam ~{normalBam} \
--tumorBam ~{tumorBam} \
--
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