diff --git a/cutadapt.wdl b/cutadapt.wdl
index 8b073442c02a449871f7dc6a320a8eabdf82d8d4..0df1ced44f253b904586c7a89b7dc61436181551 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -61,10 +61,12 @@ task Cutadapt {
String? reportPath
}
+ String read2outputArg = if (defined(read2output)) then "mkdir -p $(dirname " + read2output + ")" else ""
+
command {
set -e -o pipefail
~{"mkdir -p $(dirname " + read1output + ")"}
- ~{"mkdir -p $(dirname " + read2output + ")"}
+ ~{read2outputArg}
~{"mkdir -p $(dirname " + reportPath + ")"}
~{preCommand}
cutadapt \
diff --git a/fastqc.wdl b/fastqc.wdl
index 6d924cf550a84640fcf3e8f9e1b555d2cf239dd7..f1d23885f210e73b2452be62b499ca6ab553ed85 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -21,10 +21,10 @@ task Fastqc {
}
# Chops of the .gz extension if present.
- String name = sub(seqFile, "\\.gz$","")
+ String name = sub(seqFile, "\.gz$","")
# This regex chops of the extension and replaces it with _fastqc for the reportdir.
# Just as fastqc does it.
- String reportDir = outdirPath + "/" + sub(basename(name), "\\.[^\\.]*$", "_fastqc")
+ String reportDir = outdirPath + "/" + sub(basename(name), "\.[^\.]*$", "_fastqc")
command {
set -e -o pipefail
diff --git a/manta.wdl b/manta.wdl
index e2c59eb425722347de5608297adc43af3cb61185..a5b024c55f8f864ea97774a82081c4e35e089df6 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -1,6 +1,6 @@
version 1.0
-task Somatic {
+task ConfigureSomatic {
input {
File tumorBam
File tumorIndex
@@ -14,9 +14,6 @@ task Somatic {
Boolean exome = false
String? preCommand
String? installDir
-
- Int cores = 1
- Int memory = 4
}
String toolCommand = if defined(installDir)
@@ -33,7 +30,22 @@ task Somatic {
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
+ }
+
+ output {
+ String runDirectory = runDir
+ }
+}
+task RunSomatic {
+ input {
+ String runDir
+ Int cores = 1
+ Int memory = 4
+ Boolean paired = true
+ }
+
+ command {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
@@ -46,10 +58,10 @@ task Somatic {
"/results/variants/candidateSmallIndels.vcf.gz.tbi"
File candidateSV = runDir + "/results/variants/candidateSV.vcf.gz"
File candidateSVindex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
- File tumorSV = if defined(normalBam)
+ File tumorSV = if paired
then runDir + "/results/variants/somaticSV.vcf.gz"
else runDir + "/results/variants/tumorSV.vcf.gz"
- File tumorSVindex = if defined(normalBam)
+ File tumorSVindex = if paired
then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
File? diploidSV = "/results/variants/diploidSV.vcf.gz"
diff --git a/picard.wdl b/picard.wdl
index 4132754149ebcab5e777f2e9d90c4266cc38db4e..9dc3709d163dc0e822b0d8fd737c4a653d58ee09 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -61,8 +61,8 @@ task CollectMultipleMetrics {
File gcBiasDetail = basename + ".gc_bias.detail_metrics"
File gcBiasPdf = basename + ".gc_bias.pdf"
File gcBiasSummary = basename + ".gc_bias.summary_metrics"
- File insertSizeHistogramPdf = basename + ".insert_size_histogram.pdf"
- File insertSize = basename + ".insert_size_metrics"
+ File? insertSizeHistogramPdf = basename + ".insert_size_histogram.pdf"
+ File? insertSize = basename + ".insert_size_metrics"
File preAdapterDetail = basename + ".pre_adapter_detail_metrics"
File preAdapterSummary = basename + ".pre_adapter_summary_metrics"
File qualityByCycle = basename + ".quality_by_cycle_metrics"
@@ -110,7 +110,7 @@ task CollectRnaSeqMetrics {
}
output {
- File chart = basename + ".RNA_Metrics.pdf"
+ File? chart = basename + ".RNA_Metrics.pdf"
File metrics = basename + ".RNA_Metrics"
}
@@ -386,6 +386,7 @@ task SortVcf {
Array[File]+ vcfFiles
String outputVcf
+ File? sequenceDict
Int memory = 4
Float memoryMultiplier = 3.0
@@ -401,7 +402,8 @@ task SortVcf {
~{toolCommand} \
SortVcf \
I=~{sep=" I=" vcfFiles} \
- O=outputVcf
+ ~{"SEQUENCE_DICTIONARY=" + sequenceDict} \
+ O=~{outputVcf}
}
output {
diff --git a/strelka.wdl b/strelka.wdl
index cc3682fffeb6bfe8c9fa5241ff04d9670cb118cc..959fabf8f5a4783986c9e9b56a4b20dd7963e4e4 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -1,6 +1,6 @@
version 1.0
-task Germline {
+task ConfigureGermline {
input {
String? preCommand
String? installDir
@@ -13,9 +13,6 @@ task Germline {
File? callRegionsIndex
Boolean exome = false
Boolean rna = false
-
- Int cores = 1
- Int memory = 4
}
String toolCommand = if defined(installDir)
@@ -32,26 +29,14 @@ task Germline {
~{"--callRegions " + callRegions} \
~{true="--exome" false="" exome} \
~{true="--rna" false="" rna}
-
- ~{runDir}/runWorkflow.py \
- -m local \
- -j ~{cores} \
- -g ~{memory}
}
output {
- File variants = runDir + "/results/variants/variants.vcf.gz"
- File variantsIndex = runDir + "/results/variants/variants.vcf.gz.tbi"
- }
-
- runtime {
- cpu: cores
- memory: memory
+ String runDirectory = runDir
}
}
-
-task Somatic {
+task ConfigureSomatic {
input {
String? preCommand
String? installDir
@@ -67,9 +52,6 @@ task Somatic {
File? indelCandidates
File? indelCandidatesIndex
Boolean exome = false
-
- Int cores = 1
- Int memory = 4
}
String toolCommand = if defined(installDir)
@@ -87,7 +69,22 @@ task Somatic {
~{"--callRegions " + callRegions} \
~{"--indelCandidates " + indelCandidates} \
~{true="--exome" false="" exome} \
+ }
+
+ output {
+ String runDirectory = runDir
+ }
+}
+task Run {
+ input {
+ String runDir
+ Int cores = 1
+ Int memory = 4
+ Boolean somatic = true
+ }
+
+ command {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
@@ -95,10 +92,14 @@ task Somatic {
}
output {
- File indelsVcf = runDir + "/results/variants/somatic.indels.vcf.gz"
- File indelsIndex = runDir + "/results/variants/somatic.indels.vcf.gz.tbi"
- File snvVcf = runDir + "/results/variants/somatic.snvs.vcf.gz"
- File snvIndex = runDir + "/results/variants/somatic.snvs.vcf.gz.tbi"
+ File? indelsVcf = runDir + "/results/variants/somatic.indels.vcf.gz"
+ File? indelsIndex = runDir + "/results/variants/somatic.indels.vcf.gz.tbi"
+ File variants = if somatic
+ then runDir + "/results/variants/somatic.snvs.vcf.gz"
+ else runDir + "/results/variants/variants.vcf.gz"
+ File variantsIndex = if somatic
+ then runDir + "/results/variants/somatic.snvs.vcf.gz.tbi"
+ else runDir + "/results/variants/variants.vcf.gz.tbi"
}
runtime {
diff --git a/vardict.wdl b/vardict.wdl
index a421fd785abb9f5786cb0c9781f294c5525c60fd..c79a768ffc1fc0a72c9c8506e20338a952a91d4d 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -22,21 +22,25 @@ task VarDict {
Int geneColumn = 4
String? preCommand
+ Int memory = 8
+ Float memoryMultiplier = 2.0
}
String toolCommand = if defined(installDir)
then installDir + "/VarDict"
else if useJavaVersion
- then "vardict-java" #probably needs memory stuff
+ then "vardict-java"
else "vardict"
command {
set -e -o pipefail
+ export JAVA_OPTS="-Xmx~{memory}G"
~{preCommand}
~{toolCommand} \
-G ~{refFasta} \
-N ~{tumorSampleName} \
-b "~{tumorBam}~{"|" + normalBam}" \
+ ~{true="" false="-z" defined(normalBam)} \
-c ~{chromosomeColumn} \
-S ~{startColumn} \
-E ~{endColumn} \
@@ -53,4 +57,8 @@ task VarDict {
output {
File vcfFile = outputVcf
}
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
}