From 964c89f10f7ff73f9379197fd062f3bbd525dd2c Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 17 Aug 2018 15:48:22 +0200
Subject: [PATCH] fix vcfstats
---
biopet.wdl | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index a3ecdd0..6336e48 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -425,7 +425,7 @@ task VcfStats {
File refFasta
File refFastaIndex
File refDict
- String outDir
+ String outputDir
File? intervals
Array[String]+? infoTags
Array[String]+? genotypeTags
@@ -455,11 +455,12 @@ task VcfStats {
command {
set -e -o pipefail
+ mkdir -p ~{outputDir}
~{preCommand}
~{toolCommand} \
-I ~{vcfFile} \
-R ~{refFasta} \
- -o ~{outDir} \
+ -o ~{outputDir} \
-t ~{localThreads} \
~{"--intervals " + intervals} \
~{true="--infoTag" false="" defined(infoTags)} ~{sep=" --infoTag " infoTags} \
@@ -480,6 +481,10 @@ task VcfStats {
sep=" --sparkConfigValue" sparkConfigValues}
}
+ output {
+ String resultsDir = outputDir
+ }
+
runtime {
cpu: localThreads
memory: ceil(memory * memoryMultiplier)
--
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