From ed6d2cf289a0ca59f2341b02a82430eb6cf0c0a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Mon, 5 Aug 2019 17:57:41 +0200
Subject: [PATCH] fix command according to style guideline add comment
---
gatk.wdl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index b4a210d..c100b46 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -446,7 +446,7 @@ task FilterMutectCalls {
FilterMutectCalls \
-R ~{referenceFasta} \
-V ~{unfilteredVcf} \
- -O ${outputVcf} \
+ -O ~{outputVcf} \
~{"--contamination-table " + contaminationTable} \
~{"--tumor-segmentation " + mafTumorSegments} \
~{"--ob-priors " + artifactPriors} \
@@ -508,7 +508,7 @@ task SplitNCigarReads {
task CombineVariants {
input {
- String installDir = "/usr"
+ String installDir = "/usr" # .jar location in the docker image
File referenceFasta
File referenceFastaFai
--
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