From 680563febf9dba81cff822f73ab599b351f3e7c6 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 28 Oct 2020 10:33:36 +0100
Subject: [PATCH] Fix bug in whatshap task
---
whatshap.wdl | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/whatshap.wdl b/whatshap.wdl
index 2ee90f5..9362459 100644
--- a/whatshap.wdl
+++ b/whatshap.wdl
@@ -45,6 +45,8 @@ task Phase {
}
command {
+ set -e
+
whatshap phase \
~{vcf} \
~{phaseInput} \
@@ -56,7 +58,8 @@ task Phase {
~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
~{if defined(chromosome) then ("--chromosome " + '"' + chromosome + '"') else ""} \
~{if defined(threshold) then ("--threshold " + '"' + threshold + '"') else ""} \
- ~{if defined(ped) then ("--ped " + '"' + ped + '"') else ""} \
+ ~{if defined(ped) then ("--ped " + '"' + ped + '"') else ""}
+
tabix -p vcf ~{outputVCF}
}
@@ -159,13 +162,16 @@ task Haplotag {
}
command {
+ set -e
+
whatshap haplotag \
~{vcf} \
~{alignments} \
~{if defined(outputFile) then ("--output " + '"' + outputFile+ '"') else ""} \
~{if defined(reference) then ("--reference " + '"' + reference + '"') else ""} \
~{if defined(regions) then ("--regions " + '"' + regions + '"') else ""} \
- ~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""} \
+ ~{if defined(sample) then ("--sample " + '"' + sample + '"') else ""}
+
python3 -c "import pysam; pysam.index('~{outputFile}')"
}
--
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