From a5010d8804155529c092fc60a752148635c9906d Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 3 Jul 2019 09:18:32 +0200
Subject: [PATCH] fix samtools
---
samtools.wdl | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index 395c9ac..dcec975 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -31,14 +31,21 @@ task BgzipAndIndex {
task Index {
input {
File bamFile
+ String bamPath = basename(bamFile)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
- String bamPath = basename(bamFile)
String bamIndexPath = sub(bamPath, "\.bam$", ".bai")
command {
- ln ~{bamFile} ~{bamPath}
+ bash -c '
+ set -e
+ # Make sure bamPath does not exist.
+ if [ ! -f ~{bamPath} ]
+ then
+ ln ~{bamFile} ~{bamPath}
+ fi
samtools index ~{bamPath} ~{bamIndexPath}
+ '
}
output {
--
GitLab