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Unverified Commit af4ccc1c authored by Cats's avatar Cats Committed by GitHub
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Merge pull request #74 from biowdl/BIOWDL-78 

add SomaticSeq
parents 2b0c491d 8eda5fed
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manta.wdl
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View file @ af4ccc1c
......@@ -40,6 +40,7 @@ task ConfigureSomatic {
task RunSomatic {
input {
String? preCommand
String runDir
Int cores = 1
Int memory = 4
......@@ -47,6 +48,8 @@ task RunSomatic {
}
command {
set -e -o pipefail
~{preCommand}
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
......
picard.wdl
+ 2
− 2
View file @ af4ccc1c
......@@ -337,8 +337,8 @@ task MarkDuplicates {
task MergeVCFs {
input {
String? preCommand
Array[File] inputVCFs
Array[File] inputVCFsIndexes
Array[File]+ inputVCFs
Array[File]+ inputVCFsIndexes
String outputVcfPath
Int? compressionLevel
String? picardJar
......
somaticseq.wdl 0 → 100644
+ 257
− 0
View file @ af4ccc1c
version 1.0
import "common.wdl" as common
task ParallelPaired {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
File? classifierSNV
File? classifierIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile tumorBam
IndexedBamFile normalBam
File? mutect2VCF
File? varscanSNV
File? varscanIndel
File? jsmVCF
File? somaticsniperVCF
File? vardictVCF
File? museVCF
File? lofreqSNV
File? lofreqIndel
File? scalpelVCF
File? strelkaSNV
File? strelkaIndel
Int threads = 1
}
command {
~{installDir}/somaticseq_parallel.py \
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
--tumor-bam-file ~{tumorBam.file} \
--normal-bam-file ~{normalBam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
~{"--jsm-vcf " + jsmVCF} \
~{"--somaticsniper-vcf " + somaticsniperVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--muse-vcf " + museVCF} \
~{"--lofreq-snv " + lofreqSNV} \
~{"--lofreq-indel " + lofreqIndel} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-snv " + strelkaSNV} \
~{"--strelka-indel " + strelkaIndel}
}
output {
File indels = outputDir + if defined(classifierIndel)
then "/SSeq.Classified.sINDEL.vcf"
else "/Consensus.sINDEL.vcf"
File snvs = outputDir + if defined(classifierSNV)
then "/SSeq.Classified.sSNV.vcf"
else "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
task ParallelPairedTrain {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
File truthSNV
File truthIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile tumorBam
IndexedBamFile normalBam
File? mutect2VCF
File? varscanSNV
File? varscanIndel
File? jsmVCF
File? somaticsniperVCF
File? vardictVCF
File? museVCF
File? lofreqSNV
File? lofreqIndel
File? scalpelVCF
File? strelkaSNV
File? strelkaIndel
Int threads = 1
}
command {
~{installDir}/somaticseq_parallel.py \
--somaticseq-train \
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
paired \
--tumor-bam-file ~{tumorBam.file} \
--normal-bam-file ~{normalBam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-snv " + varscanSNV} \
~{"--varscan-indel " + varscanIndel} \
~{"--jsm-vcf " + jsmVCF} \
~{"--somaticsniper-vcf " + somaticsniperVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--muse-vcf " + museVCF} \
~{"--lofreq-snv " + lofreqSNV} \
~{"--lofreq-indel " + lofreqIndel} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-snv " + strelkaSNV} \
~{"--strelka-indel " + strelkaIndel}
}
output {
File consensusIndels = outputDir + "/Consensus.sINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
File ensembleIndelsClassifier = outputDir + "/Ensemble.sINDEL.tsv.ntChange.Classifier.RData"
File ensembleSNVClassifier = outputDir + "/Ensemble.sSNV.tsv.ntChange.Classifier.RData"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
task ParallelSingle {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
File? classifierSNV
File? classifierIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile bam
File? mutect2VCF
File? varscanVCF
File? vardictVCF
File? lofreqVCF
File? scalpelVCF
File? strelkaVCF
Int threads = 1
}
command {
~{installDir}/somaticseq_parallel.py \
~{"--classifier-snv " + classifierSNV} \
~{"--classifier-indel " + classifierIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
--bam-file ~{bam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--lofreq-vcf " + lofreqVCF} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-vcf " + strelkaVCF}
}
output {
File indels = outputDir + if defined(classifierIndel)
then "/SSeq.Classified.sINDEL.vcf"
else "/Consensus.sINDEL.vcf"
File snvs = outputDir + if defined(classifierSNV)
then "/SSeq.Classified.sSNV.vcf"
else "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
task ParallelSingleTrain {
input {
String installDir = "/opt/somaticseq" #the location in the docker image
File truthSNV
File truthIndel
String outputDir
Reference reference
File? inclusionRegion
File? exclusionRegion
IndexedBamFile bam
File? mutect2VCF
File? varscanVCF
File? vardictVCF
File? lofreqVCF
File? scalpelVCF
File? strelkaVCF
Int threads = 1
}
command {
~{installDir}/somaticseq_parallel.py \
--somaticseq-train \
--truth-snv ~{truthSNV} \
--truth-indel ~{truthIndel} \
--output-directory ~{outputDir} \
--genome-reference ~{reference.fasta} \
~{"--inclusion-region " + inclusionRegion} \
~{"--exclusion-region " + exclusionRegion} \
--threads ~{threads} \
single \
--bam-file ~{bam.file} \
~{"--mutect2-vcf " + mutect2VCF} \
~{"--varscan-vcf " + varscanVCF} \
~{"--vardict-vcf " + vardictVCF} \
~{"--lofreq-vcf " + lofreqVCF} \
~{"--scalpel-vcf " + scalpelVCF} \
~{"--strelka-vcf " + strelkaVCF}
}
output {
File consensusIndels = outputDir + "/Consensus.sINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.sSNV.vcf"
File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
File ensembleIndelsClassifier = outputDir + "/Ensemble.sINDEL.tsv.ntChange.Classifier.RData"
File ensembleSNVClassifier = outputDir + "/Ensemble.sSNV.tsv.ntChange.Classifier.RData"
}
runtime {
cpu: threads
docker: "lethalfang/somaticseq:3.1.0"
}
}
strelka.wdl
+ 3
− 0
View file @ af4ccc1c
......@@ -77,6 +77,7 @@ task ConfigureSomatic {
task Run {
input {
String? preCommand
String runDir
Int cores = 1
Int memory = 4
......@@ -85,6 +86,8 @@ task Run {
}
command {
set -e -o pipefail
~{preCommand}
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
......
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