From 24520e97a9ffef02862c36b02bcfb2a542d79086 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 12 Apr 2018 14:21:59 +0200
Subject: [PATCH] fix Map key issue star
---
star.wdl | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/star.wdl b/star.wdl
index 9e01477..d7d3b7b 100644
--- a/star.wdl
+++ b/star.wdl
@@ -18,6 +18,9 @@ task Star {
#TODO needs to be extended for all possible output extensions
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
+ # converts String? to String for use as key (for the Map above) in output
+ String key = select_first([outSAMtype, "BAM SortedByCoordinate"])
+
command {
set -e -o pipefail
mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
@@ -35,7 +38,7 @@ task Star {
}
output {
- File bamFile = outFileNamePrefix + "Aligned." + samOutputNames["${outSAMtype}"]
+ File bamFile = outFileNamePrefix + "Aligned." + samOutputNames[key]
}
runtime {
--
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