From ef2914cbdf6e935c9b4ebe499f30354b2dae9d6a Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 16:54:56 +0200
Subject: [PATCH] output file should not be optional
---
samtools.wdl | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/samtools.wdl b/samtools.wdl
index ecff136..5bb6d09 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -122,7 +122,7 @@ task view {
String? preCommand
File inFile
File? referenceFasta
- String? outputFileName
+ String outputFileName
Boolean? outputBam
Boolean? uncompressedBamOutput
Int? includeFilter
@@ -144,4 +144,8 @@ task view {
${"--threads " + threads - 1} \
${inFile}
}
+
+ output {
+ File outputFile = outputFileName
+ }
}
--
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