From 1dbfac51511fa8b15d6ff868acf18f7f52c266b4 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:32:21 +0200
Subject: [PATCH] macs2 and htseq.wdl to 1.0
---
htseq.wdl | 36 ++++++++++++++++++++----------------
macs2.wdl | 29 ++++++++++++++++-------------
2 files changed, 36 insertions(+), 29 deletions(-)
diff --git a/htseq.wdl b/htseq.wdl
index b634bf5..87c4c67 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -1,25 +1,29 @@
+version 1.0
+
task HTSeqCount {
- String? preCommand
- Array[File] alignmentFiles
- File gtfFile
- String outputTable
- String? format
- String? order
- String? stranded
+ input {
+ String? preCommand
+ Array[File] alignmentFiles
+ File gtfFile
+ String outputTable
+ String? format
+ String? order
+ String? stranded
- Int? memory
+ Int? memory
+ }
command {
set -e -o pipefail
- mkdir -p ${sub(outputTable, basename(outputTable), "")}
- ${preCommand}
+ mkdir -p ~{sub(outputTable, basename(outputTable), "")}
+ ~{preCommand}
htseq-count \
- -f ${default="bam" format} \
- -r ${default="pos" order} \
- -s ${default="no" stranded} \
- ${sep=" " alignmentFiles} \
- ${gtfFile} \
- > ${outputTable}
+ -f ~{default="bam" format} \
+ -r ~{default="pos" order} \
+ -s ~{default="no" stranded} \
+ ~{sep=" " alignmentFiles} \
+ ~{gtfFile} \
+ > ~{outputTable}
}
output {
diff --git a/macs2.wdl b/macs2.wdl
index 9880c94..026b418 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -1,20 +1,23 @@
-task PeakCalling {
- String? preCommand
- Array[File] bamFiles
- String outDir
- String sampleName
- Int? threads
- Int? memory
- Boolean? nomodel
+version 1.0
+task PeakCalling {
+ input {
+ String? preCommand
+ Array[File] bamFiles
+ String outDir
+ String sampleName
+ Int? threads
+ Int? memory
+ Boolean? nomodel
+ }
command {
set -e -o pipefail
- ${preCommand}
+ ~{preCommand}
macs2 callpeak \
- --treatment ${sep = ' ' bamFiles} \
- --outdir ${outDir} \
- --name ${sampleName} \
- ${default=false true='--nomodel' false='' nomodel}
+ --treatment ~{sep = ' ' bamFiles} \
+ --outdir ~{outDir} \
+ --name ~{sampleName} \
+ ~{default=false true='--nomodel' false='' nomodel}
}
output {
--
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