From 6aeba6149b7bb68d61141a8dc45114ad84d2615f Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 2 Sep 2019 10:51:54 +0200
Subject: [PATCH] Higher mem requirement, more concise bash invocation
---
gatk.wdl | 13 +++++--------
1 file changed, 5 insertions(+), 8 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 7b1c62e..9504de2 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -267,7 +267,7 @@ task MuTect2 {
String outputStats = outputVcf + ".stats"
Int memory = 4
- Float memoryMultiplier = 3
+ Float memoryMultiplier = 4
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -531,8 +531,9 @@ task CombineVariants {
mkdir -p $(dirname "~{outputPath}")
# build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
- # echoing the commands into a file is a workaround to avoid syntax errors when using shell
- echo '#!/bin/bash
+ # Make sure commands are run in bash
+ bash -c '#!/usr/bin/env bash
+ set -eux
ids=(~{sep=" " identifiers})
vars=(~{sep=" " variantVcfs})
V_args=$(
@@ -548,11 +549,7 @@ task CombineVariants {
--filteredrecordsmergetype ~{filteredRecordsMergeType} \
--out ~{outputPath} \
$V_args
- ' > run_combine.sh
-
- chmod 700 run_combine.sh
-
- ./run_combine.sh
+ '
>>>
output {
--
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