From ee155ce8160b16c63e0662206f22d8498d115503 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Fri, 16 Mar 2018 13:43:30 +0100
Subject: [PATCH] make outputs write to files and prefix is a must
---
biopet.wdl | 4 ++--
htseq.wdl | 10 +++++-----
stringtie.wdl | 6 ++++--
3 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 129d597..f2ca0a0 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -85,7 +85,7 @@ task BaseCounter {
File bam
File refFlat
String outputDir
- String? prefix
+ String prefix
command {
set -e -o pipefail
@@ -95,7 +95,7 @@ task BaseCounter {
-b ${bam} \
-r ${refFlat} \
-o ${outputDir} \
- ${"-p" + prefix}
+ -p ${prefix}
}
output {
diff --git a/htseq.wdl b/htseq.wdl
index bce09a8..b740b4f 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -1,13 +1,12 @@
task HTSeqCount {
+ String? preCommand
Array[File] alignmentFiles
File gffFile
-
+ String outputTable
String? format
String? order
String? stranded
- String? preCommand
-
command {
set -e -o pipefail
${preCommand}
@@ -16,10 +15,11 @@ task HTSeqCount {
-r ${default="pos" order} \
-s ${default="no" stranded} \
${sep=" " alignmentFiles} \
- ${gffFile}
+ ${gffFile} \
+ > ${outputTable}
}
output {
- File counts = stdout()
+ File counts = outputTable
}
}
\ No newline at end of file
diff --git a/stringtie.wdl b/stringtie.wdl
index a057e19..e8c74d7 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -3,6 +3,7 @@ task Stringtie {
File alignedReads
File? referenceGFF
Int? threads
+ String assembledTranscripts
command {
set -e -o pipefail
@@ -10,11 +11,12 @@ task Stringtie {
stringtie \
${"-p " + threads} \
${"-G " + referenceGFF} \
- ${alignedReads}
+ ${alignedReads} \
+ > ${assembledTranscripts}
}
output {
- File assembledTranscripts = stdout()
+ File assembledTranscripts = assembledTranscripts
}
runtime {
--
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