From a702288af9c2319eff354f3c9cce1352262d82c0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 13 Sep 2018 10:26:17 +0200
Subject: [PATCH] Fixing arguments
---
manta.wdl | 2 +-
strelka.wdl | 30 +++++++++++++++---------------
2 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/manta.wdl b/manta.wdl
index 5b8b1cd..4509cc5 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -62,7 +62,7 @@ task RunSomatic {
file: runDir + "/results/variants/candidateSV.vcf.gz",
index: runDir + "/results/variants/candidateSV.vcf.gz.tbi"
}
- File tumorSV = if (paired)
+ IndexedVcfFile tumorSV = if (paired)
then object {
file: runDir + "/results/variants/somaticSV.vcf.gz",
index: runDir + "/results/variants/somaticSV.vcf.gz.tbi"
diff --git a/strelka.wdl b/strelka.wdl
index 959fabf..c47345e 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -1,5 +1,7 @@
version 1.0
+import "common.wdl" as common
+
task ConfigureGermline {
input {
String? preCommand
@@ -7,8 +9,7 @@ task ConfigureGermline {
String runDir
Array[File]+ bams
Array[File]+ indexes
- File refFasta
- File refFastaIndex
+ Reference reference
File? callRegions
File? callRegionsIndex
Boolean exome = false
@@ -24,7 +25,7 @@ task ConfigureGermline {
~{preCommand}
~{toolCommand} \
--bam ~{sep=" --bam " bams} \
- --ref ~{refFasta} \
+ --ref ~{reference.fasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
~{true="--exome" false="" exome} \
@@ -41,16 +42,12 @@ task ConfigureSomatic {
String? preCommand
String? installDir
String runDir
- File normalBam
- File normalIndex
- File tumorBam
- File tumorIndex
- File refFasta
- File refFastaIndex
+ IndexedBamFile normalBam
+ IndexedBamFile tumorBam
+ Reference reference
File? callRegions
File? callRegionsIndex
- File? indelCandidates
- File? indelCandidatesIndex
+ IndexedVcfFile? indelCandidates
Boolean exome = false
}
@@ -58,16 +55,18 @@ task ConfigureSomatic {
then installDir + "bin/configureStrelkaSomaticWorkflow.py"
else "configureStrelkaSomaticWorkflow.py"
+ String indelCandidatesArg = if (defined(indelCandidates)) then "--indelCandidates " + select_first([indelCandidates]).file else ""
+
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
- --normalBam ~{normalBam} \
- --tumorBam ~{tumorBam} \
- --ref ~{refFasta} \
+ --normalBam ~{normalBam.file} \
+ --tumorBam ~{tumorBam.file} \
+ --ref ~{reference.fasta} \
--runDir ~{runDir} \
~{"--callRegions " + callRegions} \
- ~{"--indelCandidates " + indelCandidates} \
+ ~{indelCandidatesArg} \
~{true="--exome" false="" exome} \
}
@@ -82,6 +81,7 @@ task Run {
Int cores = 1
Int memory = 4
Boolean somatic = true
+ #FIXME: This task does not have input files
}
command {
--
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