From 26bf1e154223e0d73f7a4bce05abe3e79aa99439 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gail.com>
Date: Thu, 15 Mar 2018 16:36:58 +0100
Subject: [PATCH] modify definition of defaults
---
star.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/star.wdl b/star.wdl
index 8aceb35..a8e2453 100644
--- a/star.wdl
+++ b/star.wdl
@@ -6,8 +6,8 @@ task Star {
String genomeDir
String outFileNamePrefix
- String? outSAMtype = "BAM SortedByCoordinate"
- String? readFilesCommand = "zcat"
+ String? outSAMtype
+ String? readFilesCommand
Int? runThreadN
String? outStd
String? twopassMode
@@ -24,8 +24,8 @@ task Star {
--readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \
--outFileNamePrefix ${outFileNamePrefix} \
--genomeDir ${genomeDir} \
- ${"--readFilesCommand " + readFilesCommand} \
- ${"--outSAMtype " + outSAMtype} \
+ --outSAMtype ${default="BAM SortedByCoordinate" outSAMtype} \
+ --readFilesCommand ${default="zcat" readFilesCommand} \
${"--runThreadN " + runThreadN} \
${"--outStd " + outStd} \
${"--twopassMode " + twopassMode} \
--
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