From 19de2c0ff7fed030ffca894aa9a981fc55a295e0 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gail.com>
Date: Thu, 15 Mar 2018 13:37:37 +0100
Subject: [PATCH] update star.wdl
---
star.wdl | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/star.wdl b/star.wdl
index 7c8c4c9..8aceb35 100644
--- a/star.wdl
+++ b/star.wdl
@@ -1,8 +1,8 @@
task Star {
String? preCommand
- File inputR1
- File? inputR2
+ Array[File] inputR1
+ Array[File]? inputR2
String genomeDir
String outFileNamePrefix
@@ -11,16 +11,17 @@ task Star {
Int? runThreadN
String? outStd
String? twopassMode
- String? outSAMattrRGline
+ Array[String]? outSAMattrRGline
- Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"} #needs to be extended for all possible values
+ #TODO needs to be extended for all possible output extensions
+ Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
command {
set -e -o pipefail
mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
${preCommand}
STAR \
- --readFilesIn ${inputR1} ${inputR2} \
+ --readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \
--outFileNamePrefix ${outFileNamePrefix} \
--genomeDir ${genomeDir} \
${"--readFilesCommand " + readFilesCommand} \
@@ -28,10 +29,14 @@ task Star {
${"--runThreadN " + runThreadN} \
${"--outStd " + outStd} \
${"--twopassMode " + twopassMode} \
- ${"--outSAMattrRGline " + outSAMattrRGline}
+ ${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline}
}
output {
File bamFile = outFileNamePrefix + "Aligned." + samOutputNames["${outSAMtype}"]
}
+
+ runtime {
+ threads: runThreadN
+ }
}
\ No newline at end of file
--
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