From 783783a97e073c1866ab6d2c04f67cadd09dfa63 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 13 Sep 2018 07:59:36 +0200
Subject: [PATCH] Fixed names
---
samtools.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index 8a5e065..ff2daf0 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -25,22 +25,22 @@ task BgzipAndIndex {
task Index {
input {
String? preCommand
- File bamFilePath
+ File bamFile
String? bamIndexPath
}
command {
set -e -o pipefail
~{preCommand}
- samtools index ~{bamFilePath} ~{bamIndexPath}
+ samtools index ~{bamFile} ~{bamIndexPath}
}
output {
IndexedBamFile outputBam = object {
- file: bamFilePath,
+ file: bamFile,
index: if defined(bamIndexPath)
then select_first([bamIndexPath])
- else bamFilePath + ".bai"
+ else bamFile + ".bai"
}
}
}
--
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