From dde60f45b67f248bdfa39d3c8f37b173b847da62 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 3 Jul 2019 09:05:47 +0200
Subject: [PATCH] improve indexing
---
samtools.wdl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index b9e7d91..395c9ac 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -34,15 +34,16 @@ task Index {
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
String bamPath = basename(bamFile)
+ String bamIndexPath = sub(bamPath, "\.bam$", ".bai")
command {
ln ~{bamFile} ~{bamPath}
- samtools index ~{bamPath}
+ samtools index ~{bamPath} ~{bamIndexPath}
}
output {
File indexedBam = bamPath
- File index = sub(bamPath, "\.bam$", ".bai")
+ File index = bamIndexPath
}
runtime {
--
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