From ebc94bdbb68203cb1722c1714c3793ad29bd46e6 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:54:04 +0200
Subject: [PATCH] stringtie to 1.0
---
stringtie.wdl | 38 +++++++++++++++++++++-----------------
1 file changed, 21 insertions(+), 17 deletions(-)
diff --git a/stringtie.wdl b/stringtie.wdl
index f5c6854..2c04233 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -1,25 +1,29 @@
+version 1.0
+
task Stringtie {
- String? preCommand
- File alignedReads
- File? referenceGtf
- Int? threads
- String assembledTranscriptsFile
- Boolean? firstStranded
- Boolean? secondStranded
- String? geneAbundanceFile
+ input {
+ String? preCommand
+ File alignedReads
+ File? referenceGtf
+ Int? threads
+ String assembledTranscriptsFile
+ Boolean? firstStranded
+ Boolean? secondStranded
+ String? geneAbundanceFile
+ }
command {
set -e -o pipefail
- mkdir -p $(dirname ${assembledTranscriptsFile})
- ${preCommand}
+ mkdir -p $(dirname ~{assembledTranscriptsFile})
+ ~{preCommand}
stringtie \
- ${"-p " + threads} \
- ${"-G " + referenceGtf} \
- ${true="--rf" false="" firstStranded} \
- ${true="fr" false="" secondStranded} \
- -o ${assembledTranscriptsFile} \
- ${"-A " + geneAbundanceFile} \
- ${alignedReads} \
+ ~{"-p " + threads} \
+ ~{"-G " + referenceGtf} \
+ ~{true="--rf" false="" firstStranded} \
+ ~{true="fr" false="" secondStranded} \
+ -o ~{assembledTranscriptsFile} \
+ ~{"-A " + geneAbundanceFile} \
+ ~{alignedReads} \
}
--
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