gatk.wdl 31.67 KiB
version 1.0
# Apply Base Quality Score Recalibration (BQSR) model
task ApplyBQSR {
input {
File inputBam
File inputBamIndex
String outputBamPath
File recalibrationReport
Array[File] sequenceGroupInterval = []
File referenceFasta
File referenceFastaDict
File referenceFastaFai
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputBamPath})"
gatk --java-options -Xmx~{javaXmx} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
-R ~{referenceFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{outputBamPath} \
-bqsr ~{recalibrationReport} \
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
}
output {
File recalibratedBam = outputBamPath
File recalibratedBamIndex = sub(outputBamPath, "\.bam$", ".bai")
File recalibratedBamMd5 = outputBamPath + ".md5"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The BAM file which should be recalibrated.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
# Generate Base Quality Score Recalibration (BQSR) model
task BaseRecalibrator { input {
File inputBam
File inputBamIndex
String recalibrationReportPath
Array[File] sequenceGroupInterval = []
Array[File] knownIndelsSitesVCFs = []
Array[File] knownIndelsSitesVCFIndexes = []
File? dbsnpVCF
File? dbsnpVCFIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{recalibrationReportPath})"
gatk --java-options -Xmx~{javaXmx} \
BaseRecalibrator \
-R ~{referenceFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{recalibrationReportPath} \
~{true="--known-sites" false="" length(knownIndelsSitesVCFs) > 0} ~{sep=" --known-sites " knownIndelsSitesVCFs} \
~{"--known-sites " + dbsnpVCF} \
~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
}
output {
File recalibrationReport = recalibrationReportPath
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
inputBamIndex: {description: "The index of the input BAM file.", category: "required"}
recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
knownIndelsSitesVCFs: {description: "VCf files with known indels.", category: "advanced"}
knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs.", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CombineGVCFs {
input {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File] intervals = []
String outputPath File referenceFasta
File referenceFastaDict
File referenceFastaFai
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
CombineGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
-V ~{sep=' -V ' gvcfFiles} \
~{true='-L' false='' length(intervals) > 0} ~{sep=' -L ' intervals}
}
output {
File outputVcf = outputPath
File outputVcfIndex = outputPath + ".tbi"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
gvcfFiles: {description: "The GVCF files to be combined.", category: "required"}
gvcfFilesIndex: {description: "The indexes for the GVCF files.", caregory: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
outputPath: {description: "The location the combined GVCF should be written to.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
# Combine multiple recalibration tables from scattered BaseRecalibrator runs
task GatherBqsrReports {
input {
Array[File] inputBQSRreports
String outputReportPath
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputReportPath})"
gatk --java-options -Xmx~{javaXmx} \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
}
output { File outputBQSRreport = outputReportPath
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBQSRreports: {description: "The BQSR reports to be merged.", category: "required"}
outputReportPath: {description: "The location of the combined BQSR report.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task GenotypeGVCFs {
input {
Array[File]+ gvcfFiles
Array[File]+ gvcfFilesIndex
Array[File]+ intervals
String outputPath
File referenceFasta
File referenceFastaDict
File referenceFastaFai
File? dbsnpVCF
File? dbsnpVCFIndex
String memory = "18G"
String javaXmx = "6G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
GenotypeGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
-V ~{sep=' -V ' gvcfFiles} \
-L ~{sep=' -L ' intervals}
}
output {
File outputVCF = outputPath
File outputVCFIndex = outputPath + ".tbi"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
gvcfFiles: {description: "The GVCF files to be genotypes.", category: "required"}
gvcfFilesIndex: {description: "The index of the input GVCF files.", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
outputPath: {description: "The location to write the output VCf file to.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"} referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
task HaplotypeCallerGvcf {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
Array[File]+ intervalList
String gvcfPath
File referenceFasta
File referenceFastaIndex
File referenceFastaDict
Float contamination = 0.0
File? dbsnpVCF
File? dbsnpVCFIndex
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{gvcfPath})"
gatk --java-options -Xmx~{javaXmx} \
HaplotypeCaller \
-R ~{referenceFasta} \
-O ~{gvcfPath} \
-I ~{sep=" -I " inputBams} \
-L ~{sep=' -L ' intervalList} \
~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpVCF} \
-contamination ~{contamination} \
-ERC GVCF
}
output {
File outputGVCF = gvcfPath
File outputGVCFIndex = gvcfPath + ".tbi"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
intervalList: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"}
gvcfPath: {description: "The location to write the output GVCF to.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaIndex: {description: "The index for the reference fasta file.", category: "required"}
contamination: {description: "Equivalent to HaplotypeCaller's `-contamination` option.", category: "advanced"}
dbsnpVCF: {description: "A dbSNP VCF.", category: "common"}
dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task MuTect2 {
input {
Array[File]+ inputBams
Array[File]+ inputBamsIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
String outputVcf
String tumorSample
String? normalSample
File? germlineResource
File? germlineResourceIndex
File? panelOfNormals
File? panelOfNormalsIndex
String f1r2TarGz = "f1r2.tar.gz"
Array[File]+ intervals
String outputStats = outputVcf + ".stats"
String memory = "16G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(dirname ~{outputVcf})"
gatk --java-options -Xmx~{javaXmx} \
Mutect2 \
-R ~{referenceFasta} \
-I ~{sep=" -I " inputBams} \
-tumor ~{tumorSample} \
~{"-normal " + normalSample} \
~{"--germline-resource " + germlineResource} \
~{"--panel-of-normals " + panelOfNormals} \
~{"--f1r2-tar-gz " + f1r2TarGz} \
-O ~{outputVcf} \
-L ~{sep=" -L " intervals}
}
output {
File vcfFile = outputVcf
File vcfFileIndex = outputVcf + ".tbi"
File f1r2File = f1r2TarGz
File stats = outputStats
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
inputBamsIndex: {description: "The indexes for the input BAM files.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
tumorSample: {description: "The name of the tumor/case sample.", category: "required"}
normalSample: {description: "The name of the normal/control sample.", category: "common"}
germlineResource: {description: "Equivalent to Mutect2's `--germline-resource` option.", category: "advanced"} germlineResourceIndex: {description: "The index for the germline resource.", category: "advanced"}
panelOfNormals: {description: "Equivalent to Mutect2's `--panel-of-normals` option.", category: "advanced"}
panelOfNormalsIndex: {description: "The index for the panel of normals.", category: "advanced"}
f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
outputStats: {description: "The location the output statistics should be written to.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{javaXmx} \
LearnReadOrientationModel \
-I ~{sep=" -I " f1r2TarGz} \
-O "artifact-priors.tar.gz"
}
output {
File artifactPriorsTable = "artifact-priors.tar.gz"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
f1r2TarGz: {description: "A f1r2TarGz file outputed by mutect2.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task MergeStats {
input {
Array[File]+ stats
String memory = "28G"
String javaXmx = "14G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{javaXmx} \
MergeMutectStats \
-stats ~{sep=" -stats " stats} \
-O "merged.stats"
}
output {
File mergedStats = "merged.stats"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
stats: {description: "Statistics files to be merged.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task GetPileupSummaries {
input {
File sampleBam
File sampleBamIndex
File variantsForContamination
File variantsForContaminationIndex
File sitesForContamination
File sitesForContaminationIndex
String outputPrefix
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{javaXmx} \
GetPileupSummaries \
-I ~{sampleBam} \
-V ~{variantsForContamination} \
-L ~{sitesForContamination} \
-O ~{outputPrefix + "-pileups.table"}
}
output {
File pileups = outputPrefix + "-pileups.table"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
sampleBam: {description: "A BAM file for which a pileup should be created.", category: "required"}
sampleBamIndex: {description: "The index of the input BAM file.", category: "required"}
variantsForContamination: {description: "A VCF file with common variants.", category: "required"}
variantsForContaminationIndex: {description: "The index for the common variants VCF file.", category: "required"}
sitesForContamination: {description: "A bed file describing regions to operate on.", category: "required"}
sitesForContaminationIndex: {description: "The index for the bed file.", category: "required"}
outputPrefix: {description: "The prefix for the ouput.", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CalculateContamination {
input {
File tumorPileups File? normalPileups
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{javaXmx} \
CalculateContamination \
-I ~{tumorPileups} \
~{"-matched " + normalPileups} \
-O "contamination.table" \
--tumor-segmentation "segments.table"
}
output {
File contaminationTable = "contamination.table"
File mafTumorSegments = "segments.table"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
tumorPileups: {description: "The pileup summary of a tumor/case sample.", category: "required"}
normalPileups: {description: "The pileup summary of the normal/control sample.", category: "common"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task FilterMutectCalls {
input {
File referenceFasta
File referenceFastaFai
File referenceFastaDict
File unfilteredVcf
File unfilteredVcfIndex
String outputVcf
File? contaminationTable
File? mafTumorSegments
File? artifactPriors
Int uniqueAltReadCount = 4
File mutect2Stats
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p "$(dirname ~{outputVcf})"
gatk --java-options -Xmx~{javaXmx} \
FilterMutectCalls \
-R ~{referenceFasta} \
-V ~{unfilteredVcf} \
-O ~{outputVcf} \
~{"--contamination-table " + contaminationTable} \
~{"--tumor-segmentation " + mafTumorSegments} \
~{"--ob-priors " + artifactPriors} \
~{"--unique-alt-read-count " + uniqueAltReadCount} \
~{"-stats " + mutect2Stats} \ --filtering-stats "filtering.stats" \
--showHidden
}
output {
File filteredVcf = outputVcf
File filteredVcfIndex = outputVcf + ".tbi"
File filteringStats = "filtering.stats"
}
runtime {
docker: dockerImage
memory: memory
}
parameter_meta {
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
unfilteredVcf: {description: "An unfiltered VCF file as produced by Mutect2.", category: "required"}
unfilteredVcfIndex: {description: "The index of the unfiltered VCF file.", category: "required"}
outputVcf: {description: "The location the filtered VCf file should be written.", category: "required"}
contaminationTable: {description: "Equivalent to FilterMutectCalls' `--contamination-table` option.", category: "advanced"}
mafTumorSegments: {description: "Equivalent to FilterMutectCalls' `--tumor-segmentation` option.", category: "advanced"}
artifactPriors: {description: "Equivalent to FilterMutectCalls' `--ob-priors` option.", category: "advanced"}
uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task SplitNCigarReads {
input {
File inputBam
File inputBamIndex
File referenceFasta
File referenceFastaDict
File referenceFastaFai
String outputBam
Array[File] intervals = []
String memory = "16G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputBam})"
gatk --java-options -Xmx~{javaXmx} \
SplitNCigarReads \
-I ~{inputBam} \
-R ~{referenceFasta} \
-O ~{outputBam} \
~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
}
output {
File bam = outputBam
File bamIndex = sub(outputBam, "\.bam$", ".bai")
}
runtime {
docker: dockerImage
memory: memory }
parameter_meta {
inputBam: {description: "The BAM file for which spliced reads should be split.", category: "required"}
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.",
category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
outputBam: {description: "The location the output BAM file should be written.", category: "required"}
intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}
task CombineVariants {
input {
File referenceFasta
File referenceFastaFai
File referenceFastaDict
String genotypeMergeOption = "UNIQUIFY"
String filteredRecordsMergeType = "KEEP_IF_ANY_UNFILTERED"
Array[String]+ identifiers
Array[File]+ variantVcfs # follow "identifiers" array order
Array[File]+ variantIndexes
String outputPath
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
command <<<
set -e
mkdir -p "$(dirname ~{outputPath})"
# build "-V:<ID> <file.vcf>" arguments according to IDs and VCFs to merge
# Make sure commands are run in bash
V_args=$(bash -c '
set -eu
ids=(~{sep=" " identifiers})
vars=(~{sep=" " variantVcfs})
for (( i = 0; i < ${#ids[@]}; ++i ))
do
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
done
')
java -Xmx~{javaXmx} -jar /usr/GenomeAnalysisTK.jar \
-T CombineVariants \
-R ~{referenceFasta} \
--genotypemergeoption ~{genotypeMergeOption} \
--filteredrecordsmergetype ~{filteredRecordsMergeType} \
--out ~{outputPath} \
$V_args
>>>
output {
File combinedVcf = outputPath
File combinedVcfIndex = outputPath + ".tbi"
}
runtime {
docker: dockerImage
memory: memory }
parameter_meta {
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
genotypeMergeOption: {description: "Equivalent to CombineVariants' `--genotypemergeoption` option.", category: "advanced"}
filteredRecordsMergeType: {description: "Equivalent to CombineVariants' `--filteredrecordsmergetype` option.", category: "advanced"}
identifiers: {description: "The sample identifiers in the same order as variantVcfs.", category: "required"}
variantVcfs: {description: "The input VCF files in the same order as identifiers.", category: "required"}
variantIndexes: {description: "The indexes of the input VCF files.", category: "required"}
outputPath: {description: "The location the output should be written to", category: "required"}
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
}