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Inputs for SVcalling

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

Required inputs

SVcalling.bamFile: File
sorted BAM file
SVcalling.bamIndex: File
BAM index(.bai) file
SVcalling.bwaIndex: BwaIndex
Struct containing the BWA reference files
SVcalling.manta.cores: Int — Default: 1
The the number of cores required to run a program
SVcalling.manta.memoryGb: Int — Default: 4
The memory required to run the manta
SVcalling.referenceFasta: File
The reference fasta file
SVcalling.referenceFastaDict: File
Sequence dictionary (.dict) file of the reference
SVcalling.referenceFastaFai: File
Fasta index (.fai) file of the reference
SVcalling.sample: String
The name of the sample

Other common inputs

SVcalling.manta.callRegions: File?
The bed file which indicates the regions to operate on.
SVcalling.manta.callRegionsIndex: File?
The index of the bed file which indicates the regions to operate on.
SVcalling.manta.exome: Boolean — Default: false
Whether or not the data is from exome sequencing.
SVcalling.outputDir: String — Default: "."
The directory the output should be written to.
SVcalling.setId.annsFile: File?
Bgzip-compressed and tabix-indexed file with annotations (see man page for details).
SVcalling.setId.annsFileIndex: File?
The index for annsFile.
SVcalling.setId.inputFileIndex: File?
The index for the input vcf or bcf.

Advanced inputs

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SVcalling.annotateDH.memory: String — Default: "15GiB"
The memory required to run the programs.
SVcalling.annotateDH.timeMinutes: Int — Default: 1440
The maximum duration (in minutes) the tool is allowed to run.
SVcalling.clever.memory: String — Default: "80GiB"
The memory required to run the programs.
SVcalling.clever.threads: Int — Default: 10
The the number of threads required to run a program.
SVcalling.clever.timeMinutes: Int — Default: 2200
The maximum amount of time the job will run in minutes.
SVcalling.delly.genotypeBcf: File?
A BCF with SVs to get genotyped in the samples.
SVcalling.delly.genotypeBcfIndex: File?
The index for the genotype BCF file.
SVcalling.delly.memory: String — Default: "15GiB"
The memory required to run the programs.
SVcalling.delly.timeMinutes: Int — Default: 600
The maximum amount of time the job will run in minutes.
SVcalling.delly2vcf.exclude: String?
Exclude sites for which the expression is true (see man page for details).
SVcalling.delly2vcf.excludeUncalled: Boolean — Default: false
Exclude sites without a called genotype (see man page for details).
SVcalling.delly2vcf.include: String?
Select sites for which the expression is true (see man page for details).
SVcalling.delly2vcf.memory: String — Default: "256MiB"
The amount of memory this job will use.
SVcalling.delly2vcf.samples: Array[String] — Default: []
A list of sample names to include.
SVcalling.delly2vcf.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.dockerImages: Map[String,String] — Default: {"bcftools": "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2", "clever": "quay.io/biowdl/clever-toolkit:2.4", "delly": "quay.io/biocontainers/delly:0.8.5--hf3ca161_0", "manta": "quay.io/biocontainers/manta:1.4.0--py27_1", "picard": "quay.io/biocontainers/picard:2.23.2--0", "samtools": "quay.io/biocontainers/samtools:1.10--h9402c20_2", "survivor": "quay.io/biocontainers/survivor:1.0.7--hd03093a_2", "smoove": "quay.io/biocontainers/smoove:0.2.5--0", "duphold": "quay.io/biocontainers/duphold:0.2.1--h516909a_1", "gridss": "quay.io/biowdl/gridss:2.12.2"}
A map describing the docker image used for the tasks.
SVcalling.excludeMisHomRef: Boolean — Default: false
Option to exclude missing and homozygous reference genotypes.
SVcalling.FilterShortReadsBam.memory: String — Default: "1GiB"
The amount of memory this job will use.
SVcalling.FilterShortReadsBam.timeMinutes: Int — Default: 1 + ceil((size(bamFile,"GiB") * 8))
The maximum amount of time the job will run in minutes.
SVcalling.getIntersections.excludeUncalled: Boolean — Default: false
Exclude sites without a called genotype (see man page for details).
SVcalling.getIntersections.include: String?
Select sites for which the expression is true (see man page for details).
SVcalling.getIntersections.memory: String — Default: "256MiB"
The amount of memory this job will use.
SVcalling.getIntersections.samples: Array[String] — Default: []
A list of sample names to include.
SVcalling.getIntersections.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.getSVtype.exclude: String?
Exclude sites for which the expression is true (see man page for details).
SVcalling.getSVtype.excludeUncalled: Boolean — Default: false
Exclude sites without a called genotype (see man page for details).
SVcalling.getSVtype.memory: String — Default: "256MiB"
The amount of memory this job will use.
SVcalling.getSVtype.samples: Array[String] — Default: []
A list of sample names to include.
SVcalling.getSVtype.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.gridss.blacklistBed: File?
A bed file with blaclisted regins.
SVcalling.gridss.gridssProperties: File?
A properties file for gridss.
SVcalling.gridss.jvmHeapSizeGb: Int — Default: 64
The size of JVM heap for assembly and variant calling
SVcalling.gridss.nonJvmMemoryGb: Int — Default: 10
The amount of memory in Gb to be requested besides JVM memory.
SVcalling.gridss.normalBai: File?
The index for normalBam.
SVcalling.gridss.normalBam: File?
The BAM file for the normal/control sample.
SVcalling.gridss.normalLabel: String?
The name of the normal sample.
SVcalling.gridss.threads: Int — Default: 12
The number of the threads to use.
SVcalling.gridss.timeMinutes: Int — Default: ceil((7200 / threads)) + 1800
The maximum amount of time the job will run in minutes.
SVcalling.gridssSvTyped.dockerImage: String — Default: "quay.io/biocontainers/bioconductor-structuralvariantannotation:1.10.0--r41hdfd78af_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
SVcalling.gridssSvTyped.memory: String — Default: "32GiB"
The amount of memory this job will use.
SVcalling.gridssSvTyped.timeMinutes: Int — Default: 240
The maximum amount of time the job will run in minutes.
SVcalling.manta.timeMinutes: Int — Default: 2880
The maximum amount of time the job will run in minutes.
SVcalling.mateclever.cleverMaxDelLength: Int — Default: 100000
The maximum deletion length to look for in Clever predictions.
SVcalling.mateclever.maxLengthDiff: Int — Default: 30
The maximum length difference between split-read and read-pair deletion to be considered identical.
SVcalling.mateclever.maxOffset: Int — Default: 150
The maximum center distance between split-read and read-pair deletion to be considered identical.
SVcalling.mateclever.memory: String — Default: "250GiB"
The memory required to run the programs.
SVcalling.mateclever.threads: Int — Default: 10
The the number of threads required to run a program.
SVcalling.mateclever.timeMinutes: Int — Default: 2880
The maximum amount of time the job will run in minutes.
SVcalling.removeFpDupDel.exclude: String?
Exclude sites for which the expression is true (see man page for details).
SVcalling.removeFpDupDel.excludeUncalled: Boolean — Default: false
Exclude sites without a called genotype (see man page for details).
SVcalling.removeFpDupDel.memory: String — Default: "256MiB"
The amount of memory this job will use.
SVcalling.removeFpDupDel.samples: Array[String] — Default: []
A list of sample names to include.
SVcalling.removeFpDupDel.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.removeMisHomRR.include: String?
Select sites for which the expression is true (see man page for details).
SVcalling.removeMisHomRR.memory: String — Default: "256MiB"
The amount of memory this job will use.
SVcalling.removeMisHomRR.samples: Array[String] — Default: []
A list of sample names to include.
SVcalling.removeMisHomRR.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.renameSample.javaXmx: String — Default: "8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SVcalling.renameSample.memory: String — Default: "9GiB"
The memory required to run the programs.
SVcalling.renameSample.timeMinutes: Int — Default: 1 + ceil((size(inputVcf,"GiB") * 2))
The maximum amount of time the job will run in minutes.
SVcalling.runClever: Boolean — Default: false
Whether or not to run clever.
SVcalling.runDupHold: Boolean — Default: false
Option to run duphold annotation and filter FP deletions and duplications.
SVcalling.runSmoove: Boolean — Default: true
Whether or not to run smoove.
SVcalling.setId.collapse: String?
Treat as identical records with <snps|indels|both|all|some|none>, see man page for details.
SVcalling.setId.columns: Array[String] — Default: []
Comma-separated list of columns or tags to carry over from the annotation file (see man page for details).
SVcalling.setId.exclude: String?
Exclude sites for which the expression is true (see man page for details).
SVcalling.setId.force: Boolean — Default: false
Continue even when parsing errors, such as undefined tags, are encountered.
SVcalling.setId.headerLines: File?
Lines to append to the VCF header (see man page for details).
SVcalling.setId.include: String?
Select sites for which the expression is true (see man page for details).
SVcalling.setId.keepSites: Boolean — Default: false
Keep sites which do not pass -i and -e expressions instead of discarding them.
SVcalling.setId.markSites: String?
Annotate sites which are present ('+') or absent ('-') in the -a file with a new INFO/TAG flag.
SVcalling.setId.memory: String — Default: "4GiB"
The amount of memory this job will use.
SVcalling.setId.noVersion: Boolean — Default: false
Do not append version and command line information to the output VCF header.
SVcalling.setId.regions: String?
Restrict to comma-separated list of regions.
SVcalling.setId.regionsFile: File?
Restrict to regions listed in a file.
SVcalling.setId.removeAnns: Array[String] — Default: []
List of annotations to remove (see man page for details).
SVcalling.setId.renameChrs: File?
rename chromosomes according to the map in file (see man page for details).
SVcalling.setId.samples: Array[String] — Default: []
List of samples for sample stats, "-" to include all samples.
SVcalling.setId.samplesFile: File?
File of samples to include.
SVcalling.setId.singleOverlaps: Boolean — Default: false
keep memory requirements low with very large annotation files.
SVcalling.setId.threads: Int — Default: 0
Number of extra decompression threads [0].
SVcalling.setId.timeMinutes: Int — Default: 60 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SVcalling.smoove.memory: String — Default: "15GiB"
The memory required to run the programs.
SVcalling.smoove.timeMinutes: Int — Default: 1440
The maximum duration (in minutes) the tool is allowed to run.
SVcalling.sort.memory: String — Default: "5GiB"
The amount of memory this job will use.
SVcalling.sort.timeMinutes: Int — Default: 1 + ceil(size(inputFile,"G")) * 5
The maximum amount of time the job will run in minutes.
SVcalling.survivor.breakpointDistance: Int — Default: 1000
The distance between pairwise breakpoints between SVs.
SVcalling.survivor.distanceBySvSize: Boolean — Default: false
A boolean to predict the pairwise distance between the SVs based on their size.
SVcalling.survivor.memory: String — Default: "24GiB"
The memory required to run the programs.
SVcalling.survivor.minSize: Int — Default: 30
The mimimum size of SV to be merged.
SVcalling.survivor.strandType: Boolean — Default: true
A boolean to include strand type of an SV to be merged.
SVcalling.survivor.svType: Boolean — Default: true
A boolean to include the type SV to be merged.
SVcalling.survivor.timeMinutes: Int — Default: 60
The maximum amount of time the job will run in minutes.
SVcalling.svtypes: Array[String] — Default: ["DEL", "DUP", "INS", "INV", "BND"]
List of svtypes to be further processed and output by the pipeline.

BioWDL: structural-variantcalling

Inputs for SVcalling

Required inputs

Other common inputs

Advanced inputs