BioWDL: somatic-variantcalling

A pipeline for somatic variantcalling.

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Inputs for Strelka

The following is an overview of all available inputs in Strelka.

Required inputs

Strelka.referenceFasta
File
The reference fasta file.
Strelka.referenceFastaDict
File
Sequence dictionary (.dict) file of the reference.
Strelka.referenceFastaFai
File
Fasta index (.fai) file of the reference.
Strelka.tumorBam
File
The BAM file for the tumor/case sample.
Strelka.tumorBamIndex
File
The index for the tumor/case sample's BAM file.

Other common inputs

Strelka.basename
String — Default: "strelka"
The basename for the output.
Strelka.controlBam
File?
The BAM file for the normal/control sample.
Strelka.controlBamIndex
File?
The index for the normal/control sample's BAM file.
Strelka.exome
Boolean — Default: false
Whether or not the data is from exome sequencing.
Strelka.outputDir
String — Default: "."
The directory to which the outputs will be written.
Strelka.regions
File?
A bed file describing the regions to operate on.
Strelka.rna
Boolean — Default: false
Whether or not the data is from RNA sequencing.
Strelka.runManta
Boolean — Default: true
Whether or not manta should be run.

Advanced inputs

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Strelka.addGTFieldIndels.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
Strelka.addGTFieldIndels.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
Strelka.addGTFieldSVs.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
Strelka.addGTFieldSVs.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
Strelka.addGTFieldVariants.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
Strelka.addGTFieldVariants.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
Strelka.bedPrepare.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
Strelka.combineVariants.dockerImage
String — Default: "broadinstitute/gatk3:3.8-1"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
Strelka.combineVariants.filteredRecordsMergeType
String — Default: "KEEP_IF_ANY_UNFILTERED"
Equivalent to CombineVariants' `--filteredrecordsmergetype` option.
Strelka.combineVariants.genotypeMergeOption
String — Default: "UNIQUIFY"
Equivalent to CombineVariants' `--genotypemergeoption` option.
Strelka.combineVariants.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Strelka.combineVariants.memory
String — Default: "13G"
The amount of memory this job will use.
Strelka.combineVariants.timeMinutes
Int — Default: 180
The maximum amount of time the job will run in minutes.
Strelka.dockerImages
Map[String,String] — Default: {"picard": "quay.io/biocontainers/picard:2.23.2--0", "chunked-scatter": "quay.io/biocontainers/chunked-scatter:1.0.0--py_0", "tabix": "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0", "manta": "quay.io/biocontainers/manta:1.4.0--py27_1", "strelka": "quay.io/biocontainers/strelka:2.9.7--0", "somaticseq": "lethalfang/somaticseq:3.1.0"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
Strelka.gatherIndels.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written
Strelka.gatherIndels.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Strelka.gatherIndels.memory
String — Default: "5G"
The amount of memory this job will use.
Strelka.gatherIndels.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
Strelka.gatherIndels.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
Strelka.gatherIndels.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
Strelka.gatherSVs.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written
Strelka.gatherSVs.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Strelka.gatherSVs.memory
String — Default: "5G"
The amount of memory this job will use.
Strelka.gatherSVs.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
Strelka.gatherSVs.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
Strelka.gatherSVs.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
Strelka.gatherVariants.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written
Strelka.gatherVariants.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Strelka.gatherVariants.memory
String — Default: "5G"
The amount of memory this job will use.
Strelka.gatherVariants.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
Strelka.gatherVariants.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
Strelka.gatherVariants.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
Strelka.indelsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
Strelka.mantaSomatic.cores
Int — Default: 1
The number of cores to use.
Strelka.mantaSomatic.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
Strelka.mantaSomatic.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
Strelka.runCombineVariants
Boolean — Default: false
Whether or not found variants should be combined into a single VCf file.
Strelka.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
Strelka.scatterList.prefix
String — Default: "scatters/scatter-"
The prefix of the ouput files. Output will be named like: .bed, in which N is an incrementing number. Default 'scatter-'. </dd>
Strelka.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
Strelka.scatterSize
Int?
The size of the scattered regions in bases. Scattering is used to speed up certain processes. The genome will be seperated into multiple chunks (scatters) which will be processed in their own job, allowing for parallel processing. Higher values will result in a lower number of jobs. The optimal value here will depend on the available resources.
Strelka.scatterSizeMillions
Int — Default: 1000
Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily
Strelka.strelkaGermline.cores
Int — Default: 1
The number of cores to use.
Strelka.strelkaGermline.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
Strelka.strelkaGermline.timeMinutes
Int — Default: 90
The maximum amount of time the job will run in minutes.
Strelka.strelkaSomatic.cores
Int — Default: 1
The number of cores to use.
Strelka.strelkaSomatic.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
Strelka.strelkaSomatic.timeMinutes
Int — Default: 90
The maximum amount of time the job will run in minutes.
Strelka.svsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
Strelka.variantsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
</dl> </details> ## Do not set these inputs! The following inputs should ***not*** be set, even though womtool may show them as being available inputs. * Strelka.indelsIndex.type * Strelka.svsIndex.type * Strelka.variantsIndex.type * Strelka.strelkaSomatic.doNotDefineThis