From 732552c47b4f8cbb72cd2a5bc1ff178d3316c688 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Thu, 21 Feb 2019 10:42:55 +0100
Subject: [PATCH] excessive newline removal
---
biopet/biopet.wdl | 1 -
gatk.wdl | 7 -------
2 files changed, 8 deletions(-)
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 8199958..3c7ac7b 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -251,7 +251,6 @@ task ScatterRegions {
String outputDirPath = "scatters"
}
-
command {
set -e -o pipefail
mkdir -p ~{outputDirPath}
diff --git a/gatk.wdl b/gatk.wdl
index c354c7d..8c5e425 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -96,10 +96,7 @@ task CombineGVCFs {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File]+ intervals
-
String outputPath
-
-
Reference reference
Int memory = 4
@@ -166,11 +163,8 @@ task GenotypeGVCFs {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File]+ intervals
-
String outputPath
-
Reference reference
-
IndexedVcfFile? dbsnpVCF
Int memory = 6
@@ -217,7 +211,6 @@ task HaplotypeCallerGvcf {
String gvcfPath
Reference reference
Float contamination = 0.0
-
IndexedVcfFile? dbsnpVCF
Int memory = 4
--
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