From 0ca15e1e2e3c2664efc9eb9a3e92439f85f47486 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Mon, 12 Aug 2019 11:43:43 +0200
Subject: [PATCH] update to run in Shark: memory values and no "-o pipefail"
---
gatk.wdl | 8 ++++----
somaticseq.wdl | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 59f08ce..2154390 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -331,8 +331,8 @@ task MergeStats {
input {
Array[File]+ stats
- Int memory = 2
- Float memoryMultiplier = 1.5
+ Int memory = 14
+ Float memoryMultiplier = 2
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -435,7 +435,7 @@ task FilterMutectCalls {
File mutect2Stats
String? extraArgs
- Int memory = 4
+ Int memory = 8
Float memoryMultiplier = 1.5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -558,4 +558,4 @@ task CombineVariants {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
}
-}
\ No newline at end of file
+}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 349c7d2..7a25a08 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -280,7 +280,7 @@ task ModifyStrelka {
}
command {
- set -e -o pipefail
+ set -e
~{installDir}/modify_Strelka.py \
-infile ~{strelkaVCF} \
--
GitLab