From 67342e0312ec8bf2fcafd8e4e7e428db11fc68dc Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 22 May 2018 13:43:37 +0200
Subject: [PATCH] expression counting fixes
---
biopet.wdl | 5 +++--
htseq.wdl | 1 +
stringtie.wdl | 1 +
3 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index c40115d..e74fc61 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -2,8 +2,9 @@
# This makes searching a lot easier.
task BaseCounter {
String? preCommand
- String tool_jar #Should this be of type File?
+ String tool_jar
File bam
+ File bamIndex
File refFlat
String outputDir
String prefix
@@ -14,8 +15,8 @@ task BaseCounter {
Int mem = ceil(select_first([memory, 12.0]))
command {
set -e -o pipefail
- ${preCommand}
mkdir -p ${outputDir}
+ ${preCommand}
java -Xmx${mem}G -jar ${tool_jar} \
-b ${bam} \
-r ${refFlat} \
diff --git a/htseq.wdl b/htseq.wdl
index 6376e3e..b634bf5 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -11,6 +11,7 @@ task HTSeqCount {
command {
set -e -o pipefail
+ mkdir -p ${sub(outputTable, basename(outputTable), "")}
${preCommand}
htseq-count \
-f ${default="bam" format} \
diff --git a/stringtie.wdl b/stringtie.wdl
index 5fdcd6d..77f287e 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -10,6 +10,7 @@ task Stringtie {
command {
set -e -o pipefail
+ mkdir -p ${sub(assembledTranscriptsFile, basename(assembledTranscriptsFile), "")}
${preCommand}
stringtie \
${"-p " + threads} \
--
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