From 5596c3daa740c40752a499dabf2b9f59c157bced Mon Sep 17 00:00:00 2001
From: jboom1 <j.boom.me@lumc.nl>
Date: Fri, 6 Sep 2019 12:42:25 +0200
Subject: [PATCH] Removed "pipefail" from command sections and altered
"secondaryAlignment" Boolean
---
minimap2.wdl | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/minimap2.wdl b/minimap2.wdl
index f01c01b..d6fa35f 100644
--- a/minimap2.wdl
+++ b/minimap2.wdl
@@ -36,7 +36,6 @@ task Indexing {
}
command {
- set -e pipefail
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
~{true="-H" false="" useHomopolymerCompressedKmer} \
@@ -93,7 +92,6 @@ task Mapping {
}
command {
- set -e pipefail
mkdir -p $(dirname ~{outputPrefix})
minimap2 \
~{"-x " + presetOption} \
@@ -105,7 +103,7 @@ task Mapping {
~{"-A " + matchingScore} \
~{"-B " + mismatchPenalty} \
~{"-u " + howToFindGTAG} \
- ~{true="--secondary=yes" false="--secondary=no" secondaryAlignment} \
+ --secondary=~{true="yes" false="no" secondaryAlignment} \
~{"-o " + outputPrefix} \
~{"-t " + cores} \
~{referenceFile} \
--
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