From 0c655aeb877af353043e6188e2d4fb6b440f4dfb Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 3 Jul 2019 10:33:23 +0200
Subject: [PATCH] fix output bam
---
samtools.wdl | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index b09f37b..0c3b589 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -31,26 +31,26 @@ task BgzipAndIndex {
task Index {
input {
File bamFile
- String? bamPath
+ String? outputBamPath
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- String bamIndexPath = sub(select_first([bamPath, basename(bamFile)]), "\.bam$", ".bai")
+ String bamIndexPath = sub(select_first([outputBamPath, basename(bamFile)]), "\.bam$", ".bai")
command {
bash -c '
set -e
- # Make sure bamPath does not exist.
- if [ ! -f ~{bamPath} ]
+ # Make sure outputBamPath does not exist.
+ if [ ! -f ~{outputBamPath} ]
then
- mkdir -p $(dirname ~{bamPath})
- ln ~{bamFile} ~{bamPath}
+ mkdir -p $(dirname ~{outputBamPath})
+ ln ~{bamFile} ~{outputBamPath}
fi
- samtools index ~{bamPath} ~{bamIndexPath}
+ samtools index ~{outputBamPath} ~{bamIndexPath}
'
}
output {
- File indexedBam = bamPath
+ File indexedBam = outputBamPath
File index = bamIndexPath
}
--
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