From 9f02ca5a1876b5b0d8403442004171379f49767f Mon Sep 17 00:00:00 2001
From: ffinfo <pjrvanthof@gmail.com>
Date: Wed, 12 Sep 2018 11:48:11 +0200
Subject: [PATCH] Fixing validate issues
---
htseq.wdl | 5 +++--
macs2.wdl | 5 +++--
manta.wdl | 4 +++-
vardict.wdl | 4 +++-
4 files changed, 12 insertions(+), 6 deletions(-)
diff --git a/htseq.wdl b/htseq.wdl
index 0e922db..cdfc984 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -5,7 +5,8 @@ import "common.wdl"
task HTSeqCount {
input {
String? preCommand
- Array[IndexedBamFile] inputBamFiles
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
File gtfFile
String outputTable
String format = "bam"
@@ -23,7 +24,7 @@ task HTSeqCount {
-f ~{format} \
-r ~{order} \
-s ~{stranded} \
- ~{sep=" " inputBamFiles.file} \
+ ~{sep=" " inputBams} \
~{gtfFile} \
> ~{outputTable}
}
diff --git a/macs2.wdl b/macs2.wdl
index 4f1e1be..982802f 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -5,7 +5,8 @@ import "common.wdl"
task PeakCalling {
input {
String? preCommand
- Array[IndexedBamFile] bamFiles
+ Array[File]+ inputBams
+ Array[File]+ inputBamsIndex
String outDir
String sampleName
Int threads = 1
@@ -17,7 +18,7 @@ task PeakCalling {
set -e -o pipefail
~{preCommand}
macs2 callpeak \
- --treatment ~{sep = ' ' bamFiles.file} \
+ --treatment ~{sep = ' ' inputBams} \
--outdir ~{outDir} \
--name ~{sampleName} \
~{true='--nomodel' false='' nomodel}
diff --git a/manta.wdl b/manta.wdl
index 3c37e5e..5b8b1cd 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -19,11 +19,13 @@ task ConfigureSomatic {
then installDir + "bin/configMata.py"
else "configManta.py"
+ String normalArg = if (defined(normalBam)) then "--normalBam " + select_first([normalBam]).file else ""
+
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
- ~{"--normalBam " + normalBam.file} \
+ ~{normalArg} \
~{"--tumorBam " + tumorBam.file} \
--referenceFasta ~{reference.fasta} \
~{"--callRegions " + callRegions} \
diff --git a/vardict.wdl b/vardict.wdl
index 0275ef1..989fc25 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -25,6 +25,8 @@ task VarDict {
Float memoryMultiplier = 2.0
}
+ String normalArg = if (defined(normalBam)) then "|" + select_first([normalBam]).file else ""
+
String toolCommand = if defined(installDir)
then installDir + "/VarDict"
else if useJavaVersion
@@ -38,7 +40,7 @@ task VarDict {
~{toolCommand} \
-G ~{reference.fasta} \
-N ~{tumorSampleName} \
- -b "~{tumorBam.file}~{"|" + normalBam.file}" \
+ -b "~{tumorBam.file}~{normalArg}" \
~{true="" false="-z" defined(normalBam)} \
-c ~{chromosomeColumn} \
-S ~{startColumn} \
--
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