From 0ad2ddbe042bf9a3520892b8980278244ccdc3db Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 15 Jun 2020 10:58:18 +0200
Subject: [PATCH] Fix command section now that new inputs are optional.
---
star.wdl | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/star.wdl b/star.wdl
index da90516..6f95a63 100644
--- a/star.wdl
+++ b/star.wdl
@@ -123,10 +123,10 @@ task Star {
--genomeDir ~{sub(indexFiles[0], basename(indexFiles[0]), "")} \
--outSAMtype ~{outSAMtype} \
--readFilesCommand ~{readFilesCommand} \
- --outFilterScoreMin ~{outFilterScoreMin} \
- --outFilterScoreMinOverLread ~{outFilterScoreMinOverLread} \
- --outFilterMatchNmin ~{outFilterMatchNmin} \
- --outFilterMatchNminOverLread ~{outFilterMatchNminOverLread} \
+ ~{"--outFilterScoreMin " + outFilterScoreMin} \
+ ~{"--outFilterScoreMinOverLread " + outFilterScoreMinOverLread} \
+ ~{"--outFilterMatchNmin " + outFilterMatchNmin} \
+ ~{"--outFilterMatchNminOverLread " + outFilterMatchNminOverLread} \
~{"--outSAMunmapped " + outSAMunmapped} \
~{"--runThreadN " + runThreadN} \
~{"--outStd " + outStd} \
--
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