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manta.wdl
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manta.wdl
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version 1.0
# Copyright (c) 2017 Leiden University Medical Center
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
task Germline {
input {
File bamFile
File bamIndex
File referenceFasta
File referenceFastaFai
String runDir = "./manta_run"
Boolean exome = false
File? callRegions
File? callRegionsIndex
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 2880
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
command {
set -e
configManta.py \
~{"--normalBam " + bamFile} \
--referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
-g ~{memoryGb}
}
output {
File mantaVCF = runDir + "/results/variants/diploidSV.vcf.gz"
File mantaVCFindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
runtime {
cpu: cores
memory: "~{memoryGb}GiB"
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
# inputs
bamFile: {description: "The bam file to process.", category: "required"}
bamIndex: {description: "The index bam file.", category: "required"}
referenceFasta: {description: "The reference fasta file also used for mapping.", category: "required"}
referenceFastaFai: {description: "Fasta index (.fai) file of the reference", category: "required" }
runDir: {description: "The directory to use as run/output directory.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
cores: {description: "The the number of cores required to run a program", category: "required"}
memoryGb: {description: "The memory required to run the manta", category: "required"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
# outputs
mantaVCF: {description: "SVs and indels scored and genotyped under a diploid model for the set of samples in a joint diploid sample analysis or for the normal sample in a tumor/normal subtraction analysis."}
mantaVCFindex: {description: "Index of output mantaVCF."}
}
}
task Somatic {
input {
File tumorBam
File tumorBamIndex
File referenceFasta
File referenceFastaFai
String runDir = "./manta_run"
Boolean exome = false
File? normalBam
File? normalBamIndex
File? callRegions
File? callRegionsIndex
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 2880
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
command {
configManta.py \
~{"--normalBam " + normalBam} \
~{"--tumorBam " + tumorBam} \
--referenceFasta ~{referenceFasta} \
~{"--callRegions " + callRegions} \
--runDir ~{runDir} \
~{true="--exome" false="" exome}
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
-g ~{memoryGb}
}
output {
File candidateSmallIndelsVcf = runDir + "/results/variants/candidateSmallIndels.vcf.gz"
File candidateSmallIndelsVcfIndex = runDir + "/results/variants/candidateSmallIndels.vcf.gz.tbi"
File candidateSVVcf = runDir + "/results/variants/candidateSV.vcf.gz"
File candidatSVVcfIndex = runDir + "/results/variants/candidateSV.vcf.gz.tbi"
File tumorSVVcf = if defined(normalBam)
then runDir + "/results/variants/somaticSV.vcf.gz"
else runDir + "/results/variants/tumorSV.vcf.gz"
File tumorSVVcfIndex = if defined(normalBam)
then runDir + "/results/variants/somaticSV.vcf.gz.tbi"
else runDir + "/results/variants/tumorSV.vcf.gz.tbi"
File? diploidSV = runDir + "/results/variants/diploidSV.vcf.gz"
File? diploidSVindex = runDir + "/results/variants/diploidSV.vcf.gz.tbi"
}
runtime {
cpu: cores
memory: "~{memoryGb}GiB"
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
# inputs
tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"}
referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
runDir: {description: "The directory to use as run/output directory.", category: "common"}
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
normalBamIndex: {description: "The index for the normal/control sample's BAM file.", category: "common"}
callRegions: {description: "The bed file which indicates the regions to operate on.", category: "common"}
callRegionsIndex: {description: "The index of the bed file which indicates the regions to operate on.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
# outputs
candidateSmallIndelsVcf: {description: "Subset of the candidateSV.vcf.gz file containing only simple insertion and deletion variants less than the minimum scored variant size."}
candidateSmallIndelsVcfIndex: {description: "Index of output VCF file candidateSmallIndelsVcf."}
candidateSVVcf: {description: "Unscored SV and indel candidates."}
candidatSVVcfIndex: {description: "Index of output VCF file candidateSVVcf."}
tumorSVVcf: {description: "Subset of the candidateSV.vcf.gz file after removing redundant candidates and small indels less than the minimum scored variant size."}
tumorSVVcfIndex: {description: "Index of output VCF file tumorSVVcf."}
diploidSV: {description: "SVs and indels scored and genotyped under a diploid model for the set of samples in a joint diploid sample analysis or for the normal sample in a tumor/normal subtraction analysis."}
diploidSVindex: {description: "Index of output VCF file diploidSV."}
}
}