From 60c48b64ab592288e9727de11a68d9a7b3cafc16 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 28 Oct 2019 14:28:21 +0100
Subject: [PATCH] fix samtools index
---
samtools.wdl | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index 7c1143c..871110d 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -31,28 +31,29 @@ task BgzipAndIndex {
task Index {
input {
File bamFile
- String outputBamPath = basename(bamFile)
+ String? outputBamPath
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
# Select_first is needed, otherwise womtool validate fails.
- String bamIndexPath = sub(select_first([outputBamPath]), "\.bam$", ".bai")
+ String outputPath = select_first([outputBamPath, basename(bamFile)])
+ String bamIndexPath = sub(outputPath, "\.bam$", ".bai")
command {
bash -c '
set -e
# Make sure outputBamPath does not exist.
- if [ ! -f ~{outputBamPath} ]
+ if [ ! -f ~{outputPath} ]
then
- mkdir -p $(dirname ~{outputBamPath})
- ln ~{bamFile} ~{outputBamPath}
+ mkdir -p $(dirname ~{outputPath})
+ ln ~{bamFile} ~{outputPath}
fi
- samtools index ~{outputBamPath} ~{bamIndexPath}
+ samtools index ~{outputPath} ~{bamIndexPath}
'
}
output {
- File indexedBam = outputBamPath
+ File indexedBam = outputPath
File index = bamIndexPath
}
--
GitLab