GATK4: VariantFiltration

Gatk4Variantfiltration · 1 contributor · 4 versions

USAGE: VariantFiltration [arguments] Filter variant calls based on INFO and/or FORMAT annotations. Version:4.1.3.0

Quickstart

from janis_bioinformatics.tools.gatk4.variantfiltration.versions import Gatk4VariantFiltration_4_1_4

wf = WorkflowBuilder("myworkflow")

wf.step(
    "gatk4variantfiltration_step",
    Gatk4VariantFiltration_4_1_4(
        variant=None,
        filterName=None,
    )
)
wf.output("out", source=gatk4variantfiltration_step.out)

OR

  1. Install Janis
  2. Ensure Janis is configured to work with Docker or Singularity.
  3. Ensure all reference files are available:

Note

More information about these inputs are available below.

  1. Generate user input files for Gatk4Variantfiltration:
# user inputs
janis inputs Gatk4Variantfiltration > inputs.yaml

inputs.yaml

filterName:
- <value>
- <value>
variant: variant.vcf.gz
  1. Run Gatk4Variantfiltration with:
janis run [...run options] \
    --inputs inputs.yaml \
    Gatk4Variantfiltration

Information

ID:Gatk4Variantfiltration
URL:No URL to the documentation was provided
Versions:4.1.4.0, 4.1.3.0, 4.1.2.0, 4.0.12.0
Container:broadinstitute/gatk:4.1.4.0
Authors:Michael Franklin
Citations:None
Created:2020-05-18
Updated:2020-05-18

Outputs

name type documentation
out Gzipped<VCF>  

Additional configuration (inputs)

name type prefix position documentation
variant Gzipped<VCF> –variant   (-V) A VCF file containing variants Required.
filterName Array<Optional<String>> –filter-name   Names to use for the list of filters This argument may be specified 0 or more times. Default value: null.
javaOptions Optional<Array<String>>      
compression_level Optional<Integer>     Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
outputFilename Optional<Filename> –output   (-O) File to which variants should be written Required.
addOutputSamProgramRecord Optional<Boolean> –add-output-sam-program-record   (-add-output-sam-program-record) If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible values: {true, false}
addOutputVcfCommandLine Optional<Boolean> –add-output-vcf-command-line   (-add-output-vcf-command-line) If true, adds a command line header line to created VCF files. Default value: true. Possible values: {true, false}
arguments_file Optional<File> –arguments_file   read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
cloudIndexPrefetchBuffer Optional<Integer> –cloud-index-prefetch-buffer   (-CIPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. Default value: -1.
cloudPrefetchBuffer Optional<Integer> –cloud-prefetch-buffer   (-CPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
clusterSize Optional<Integer> –cluster-size   (-cluster) The number of SNPs which make up a cluster. Must be at least 2 Default value: 3.
clusterWindowSize Optional<Integer> –cluster-window-size   (-window) The window size (in bases) in which to evaluate clustered SNPs Default value: 0.
createOutputBamIndex Optional<Boolean> –create-output-bam-index   (-OBI) If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default value: true. Possible values: {true, false}
createOutputBamMd5 Optional<Boolean> –create-output-bam-md5   (-OBM) If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false. Possible values: {true, false}
createOutputVariantIndex Optional<Boolean> –create-output-variant-index   (-OVI) If true, create a VCF index when writing a coordinate-sorted VCF file. Default value: true. Possible values: {true, false}
createOutputVariantMd5 Optional<Boolean> –create-output-variant-md5   (-OVM) If true, create a a MD5 digest any VCF file created. Default value: false. Possible values: {true, false}
disableBamIndexCaching Optional<Boolean> –disable-bam-index-caching   (-DBIC) If true, don’t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. Default value: false. Possible values: {true, false}
disableReadFilter Optional<String> –disable-read-filter   (-DF) Read filters to be disabled before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {WellformedReadFilter}
disableSequenceDictionaryValidation Optional<Boolean> –disable-sequence-dictionary-validation   (-disable-sequence-dictionary-validation) If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! Default value: false. Possible values: {true, false}
excludeIntervals Optional<Boolean> –exclude-intervals   (-XL) This argument may be specified 0 or more times. Default value: null.
filterExpression Optional<Array<String>> –filter-expression   (-filter) One or more expressions used with INFO fields to filter This argument may be specified 0 or more times. Default value: null.
filterNotInMask Optional<Boolean> –filter-not-in-mask   Filter records NOT in given input mask. Default value: false. Possible values: {true, false}
gatkConfigFile Optional<String> –gatk-config-file   A configuration file to use with the GATK. Default value: null.
gcsMaxRetries Optional<Integer> –gcs-max-retries   (-gcs-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20.
gcsProjectForRequesterPays Optional<String> –gcs-project-for-requester-pays   Project to bill when accessing ‘requester pays’ buckets. If unset, these buckets cannot be accessed. Default value: .
genotypeFilterExpression Optional<String> –genotype-filter-expression   (-G-filter) One or more expressions used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info) This argument may be specified 0 or more times. Default value: null.
genotypeFilterName Optional<String> –genotype-filter-name   (-G-filter-name) Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered This argument may be specified 0 or more times. Default value: null.
help Optional<Boolean> –help   (-h) display the help message Default value: false. Possible values: {true, false}
inp Optional<String> –input   (-I) BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times. Default value: null.
intervalExclusionPadding Optional<Integer> –interval-exclusion-padding   (-ixp) Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
intervalMergingRule Optional<Boolean> –interval-merging-rule   (-imr) Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY}
intervalPadding Optional<Boolean> –interval-padding   (-ip) Default value: 0.
intervalSetRule Optional<Boolean> –interval-set-rule   (-isr) Set merging approach to use for combining interval inputs Default value: UNION. Possible values: {UNION, INTERSECTION}
intervals Optional<String> –intervals   (-L) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null.
invalidatePreviousFilters Optional<Boolean> –invalidate-previous-filters   Remove previous filters applied to the VCF Default value: false. Possible values: {true, false}
invertFilterExpression Optional<Boolean> –invert-filter-expression   (-invfilter) Invert the selection criteria for –filter-expression Default value: false. Possible values: {true, false}
invertGenotypeFilterExpression Optional<Boolean> –invert-genotype-filter-expression   (-invG-filter) Invert the selection criteria for –genotype-filter-expression Default value: false. Possible values: {true, false}
lenient Optional<Boolean> –lenient   (-LE) Lenient processing of VCF files Default value: false. Possible values: {true, false}
mask Optional<Boolean> –mask   (-mask) Input mask Default value: null.
maskExtension Optional<Integer> –mask-extension   How many bases beyond records from a provided ‘mask’ should variants be filtered Default value: 0.
maskName Optional<String> –mask-name   The text to put in the FILTER field if a ‘mask’ is provided and overlaps with a variant call Default value: Mask.
missingValuesEvaluateAsFailing Optional<Boolean> –missing-values-evaluate-as-failing   When evaluating the JEXL expressions, missing values should be considered failing the expression Default value: false. Possible values: {true, false}
quiet Optional<Boolean> –QUIET   Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
readFilter Optional<String> –read-filter   (-RF) Read filters to be applied before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter, AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator, FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter, MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter, MetricsReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter}
readIndex Optional<String> –read-index   (-read-index) Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. This argument may be specified 0 or more times. Default value: null.
readValidationStringency Optional<Boolean> –read-validation-stringency   (-VS) Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
reference Optional<FastaWithIndexes> –reference   (-R) Reference sequence Default value: null.
secondsBetweenProgressUpdates Optional<Double> –seconds-between-progress-updates   (-seconds-between-progress-updates) Output traversal statistics every time this many seconds elapse Default value: 10.0.
sequenceDictionary Optional<String> –sequence-dictionary   (-sequence-dictionary) Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. Default value: null.
setFilteredGenotypeToNoCall Optional<Boolean> –set-filtered-genotype-to-no-call   Set filtered genotypes to no-call Default value: false. Possible values: {true, false}
sitesOnlyVcfOutput Optional<Boolean> –sites-only-vcf-output   If true, don’t emit genotype fields when writing vcf file output. Default value: false. Possible values: {true, false}
tmpDir Optional<Boolean> –tmp-dir   Temp directory to use. Default value: null.
useJdkDeflater Optional<Boolean> –use-jdk-deflater   (-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false}
useJdkInflater Optional<Boolean> –use-jdk-inflater   (-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false}
verbosity Optional<Boolean> –verbosity   (-verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
version Optional<Boolean> –version   display the version number for this tool Default value: false. Possible values: {true, false}
disableToolDefaultReadFilters Optional<Boolean> –disable-tool-default-read-filters   (-disable-tool-default-read-filters) Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) Default value: false. Possible values: {true, false}
showhidden Optional<Boolean> –showHidden   (-showHidden) display hidden arguments Default value: false. Possible values: {true, false}
ambigFilterBases Optional<Integer> –ambig-filter-bases   Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction. Default value: null. Cannot be used in conjuction with argument(s) maxAmbiguousBaseFraction
ambigFilterFrac Optional<Double> –ambig-filter-frac   Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases
maxFragmentLength Optional<Boolean> –max-fragment-length   Default value: 1000000.
minFragmentLength Optional<Boolean> –min-fragment-length   Default value: 0.
keepIntervals Optional<String> –keep-intervals   One or more genomic intervals to keep This argument must be specified at least once. Required.
library Optional<String> –library   (-library) Name of the library to keep This argument must be specified at least once. Required.
maximumMappingQuality Optional<Integer> –maximum-mapping-quality   Maximum mapping quality to keep (inclusive) Default value: null.
minimumMappingQuality Optional<Integer> –minimum-mapping-quality   Minimum mapping quality to keep (inclusive) Default value: 10.
dontRequireSoftClipsBothEnds Optional<Boolean> –dont-require-soft-clips-both-ends   Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block Default value: false. Possible values: {true, false}
filterTooShort Optional<Integer> –filter-too-short   Minimum number of aligned bases Default value: 30.
platformFilterName Optional<Boolean> –platform-filter-name   This argument must be specified at least once. Required.
blackListedLanes Optional<String> –black-listed-lanes   Platform unit (PU) to filter out This argument must be specified at least once. Required.
readGroupBlackList Optional<Boolean> –read-group-black-list   This argument must be specified at least once. Required.
keepReadGroup Optional<String> –keep-read-group   The name of the read group to keep Required.
maxReadLength Optional<Integer> –max-read-length   Keep only reads with length at most equal to the specified value Required.
minReadLength Optional<Integer> –min-read-length   Keep only reads with length at least equal to the specified value Default value: 1.
readName Optional<String> –read-name   Keep only reads with this read name Required.
keepReverseStrandOnly Optional<Boolean> –keep-reverse-strand-only   Keep only reads on the reverse strand Required. Possible values: {true, false}
sample Optional<String> –sample   (-sample) The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required.
invertSoftClipRatioFilter Optional<Boolean> –invert-soft-clip-ratio-filter   Inverts the results from this filter, causing all variants that would pass to fail and visa-versa. Default value: false. Possible values: {true, false}
softClippedLeadingTrailingRatio Optional<Double> –soft-clipped-leading-trailing-ratio   Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumSoftClippedRatio
softClippedRatioThreshold Optional<Double> –soft-clipped-ratio-threshold   Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumLeadingTrailingSoftClippedRatio

Workflow Description Language

version development

task Gatk4Variantfiltration {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[String]? javaOptions
    Int? compression_level
    String? outputFilename
    File variant
    File variant_tbi
    Boolean? addOutputSamProgramRecord
    Boolean? addOutputVcfCommandLine
    File? arguments_file
    Int? cloudIndexPrefetchBuffer
    Int? cloudPrefetchBuffer
    Int? clusterSize
    Int? clusterWindowSize
    Boolean? createOutputBamIndex
    Boolean? createOutputBamMd5
    Boolean? createOutputVariantIndex
    Boolean? createOutputVariantMd5
    Boolean? disableBamIndexCaching
    String? disableReadFilter
    Boolean? disableSequenceDictionaryValidation
    Boolean? excludeIntervals
    Array[String]? filterExpression
    Array[String?] filterName
    Boolean? filterNotInMask
    String? gatkConfigFile
    Int? gcsMaxRetries
    String? gcsProjectForRequesterPays
    String? genotypeFilterExpression
    String? genotypeFilterName
    Boolean? help
    String? inp
    Int? intervalExclusionPadding
    Boolean? intervalMergingRule
    Boolean? intervalPadding
    Boolean? intervalSetRule
    String? intervals
    Boolean? invalidatePreviousFilters
    Boolean? invertFilterExpression
    Boolean? invertGenotypeFilterExpression
    Boolean? lenient
    Boolean? mask
    Int? maskExtension
    String? maskName
    Boolean? missingValuesEvaluateAsFailing
    Boolean? quiet
    String? readFilter
    String? readIndex
    Boolean? readValidationStringency
    File? reference
    File? reference_fai
    File? reference_amb
    File? reference_ann
    File? reference_bwt
    File? reference_pac
    File? reference_sa
    File? reference_dict
    Float? secondsBetweenProgressUpdates
    String? sequenceDictionary
    Boolean? setFilteredGenotypeToNoCall
    Boolean? sitesOnlyVcfOutput
    Boolean? tmpDir
    Boolean? useJdkDeflater
    Boolean? useJdkInflater
    Boolean? verbosity
    Boolean? version
    Boolean? disableToolDefaultReadFilters
    Boolean? showhidden
    Int? ambigFilterBases
    Float? ambigFilterFrac
    Boolean? maxFragmentLength
    Boolean? minFragmentLength
    String? keepIntervals
    String? library
    Int? maximumMappingQuality
    Int? minimumMappingQuality
    Boolean? dontRequireSoftClipsBothEnds
    Int? filterTooShort
    Boolean? platformFilterName
    String? blackListedLanes
    Boolean? readGroupBlackList
    String? keepReadGroup
    Int? maxReadLength
    Int? minReadLength
    String? readName
    Boolean? keepReverseStrandOnly
    String? sample
    Boolean? invertSoftClipRatioFilter
    Float? softClippedLeadingTrailingRatio
    Float? softClippedRatioThreshold
  }
  command <<<
    set -e
    gatk VariantFiltration \
      --java-options '-Xmx~{((select_first([runtime_memory, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
      --output '~{select_first([outputFilename, "~{basename(variant, ".vcf.gz")}.filtered.vcf"])}' \
      --variant '~{variant}' \
      ~{if (defined(addOutputSamProgramRecord) && select_first([addOutputSamProgramRecord])) then "--add-output-sam-program-record" else ""} \
      ~{if (defined(addOutputVcfCommandLine) && select_first([addOutputVcfCommandLine])) then "--add-output-vcf-command-line" else ""} \
      ~{if defined(arguments_file) then ("--arguments_file '" + arguments_file + "'") else ""} \
      ~{if defined(cloudIndexPrefetchBuffer) then ("--cloud-index-prefetch-buffer " + cloudIndexPrefetchBuffer) else ''} \
      ~{if defined(cloudPrefetchBuffer) then ("--cloud-prefetch-buffer " + cloudPrefetchBuffer) else ''} \
      ~{if defined(clusterSize) then ("--cluster-size " + clusterSize) else ''} \
      ~{if defined(clusterWindowSize) then ("--cluster-window-size " + clusterWindowSize) else ''} \
      ~{if (defined(createOutputBamIndex) && select_first([createOutputBamIndex])) then "--create-output-bam-index" else ""} \
      ~{if (defined(createOutputBamMd5) && select_first([createOutputBamMd5])) then "--create-output-bam-md5" else ""} \
      ~{if (defined(createOutputVariantIndex) && select_first([createOutputVariantIndex])) then "--create-output-variant-index" else ""} \
      ~{if (defined(createOutputVariantMd5) && select_first([createOutputVariantMd5])) then "--create-output-variant-md5" else ""} \
      ~{if (defined(disableBamIndexCaching) && select_first([disableBamIndexCaching])) then "--disable-bam-index-caching" else ""} \
      ~{if defined(disableReadFilter) then ("--disable-read-filter '" + disableReadFilter + "'") else ""} \
      ~{if (defined(disableSequenceDictionaryValidation) && select_first([disableSequenceDictionaryValidation])) then "--disable-sequence-dictionary-validation" else ""} \
      ~{if (defined(excludeIntervals) && select_first([excludeIntervals])) then "--exclude-intervals" else ""} \
      ~{if (defined(filterExpression) && length(select_first([filterExpression])) > 0) then "--filter-expression '" + sep("' --filter-expression '", select_first([filterExpression])) + "'" else ""} \
      ~{if length(filterName) > 0 then "--filter-name '" + sep("' --filter-name '", select_all(filterName)) + "'" else ""} \
      ~{if (defined(filterNotInMask) && select_first([filterNotInMask])) then "--filter-not-in-mask" else ""} \
      ~{if defined(gatkConfigFile) then ("--gatk-config-file '" + gatkConfigFile + "'") else ""} \
      ~{if defined(gcsMaxRetries) then ("--gcs-max-retries " + gcsMaxRetries) else ''} \
      ~{if defined(gcsProjectForRequesterPays) then ("--gcs-project-for-requester-pays '" + gcsProjectForRequesterPays + "'") else ""} \
      ~{if defined(genotypeFilterExpression) then ("--genotype-filter-expression '" + genotypeFilterExpression + "'") else ""} \
      ~{if defined(genotypeFilterName) then ("--genotype-filter-name '" + genotypeFilterName + "'") else ""} \
      ~{if (defined(help) && select_first([help])) then "--help" else ""} \
      ~{if defined(inp) then ("--input '" + inp + "'") else ""} \
      ~{if defined(intervalExclusionPadding) then ("--interval-exclusion-padding " + intervalExclusionPadding) else ''} \
      ~{if (defined(intervalMergingRule) && select_first([intervalMergingRule])) then "--interval-merging-rule" else ""} \
      ~{if (defined(intervalPadding) && select_first([intervalPadding])) then "--interval-padding" else ""} \
      ~{if (defined(intervalSetRule) && select_first([intervalSetRule])) then "--interval-set-rule" else ""} \
      ~{if defined(intervals) then ("--intervals '" + intervals + "'") else ""} \
      ~{if (defined(invalidatePreviousFilters) && select_first([invalidatePreviousFilters])) then "--invalidate-previous-filters" else ""} \
      ~{if (defined(invertFilterExpression) && select_first([invertFilterExpression])) then "--invert-filter-expression" else ""} \
      ~{if (defined(invertGenotypeFilterExpression) && select_first([invertGenotypeFilterExpression])) then "--invert-genotype-filter-expression" else ""} \
      ~{if (defined(lenient) && select_first([lenient])) then "--lenient" else ""} \
      ~{if (defined(mask) && select_first([mask])) then "--mask" else ""} \
      ~{if defined(maskExtension) then ("--mask-extension " + maskExtension) else ''} \
      ~{if defined(maskName) then ("--mask-name '" + maskName + "'") else ""} \
      ~{if (defined(missingValuesEvaluateAsFailing) && select_first([missingValuesEvaluateAsFailing])) then "--missing-values-evaluate-as-failing" else ""} \
      ~{if (defined(quiet) && select_first([quiet])) then "--QUIET" else ""} \
      ~{if defined(readFilter) then ("--read-filter '" + readFilter + "'") else ""} \
      ~{if defined(readIndex) then ("--read-index '" + readIndex + "'") else ""} \
      ~{if (defined(readValidationStringency) && select_first([readValidationStringency])) then "--read-validation-stringency" else ""} \
      ~{if defined(reference) then ("--reference '" + reference + "'") else ""} \
      ~{if defined(secondsBetweenProgressUpdates) then ("--seconds-between-progress-updates " + secondsBetweenProgressUpdates) else ''} \
      ~{if defined(sequenceDictionary) then ("--sequence-dictionary '" + sequenceDictionary + "'") else ""} \
      ~{if (defined(setFilteredGenotypeToNoCall) && select_first([setFilteredGenotypeToNoCall])) then "--set-filtered-genotype-to-no-call" else ""} \
      ~{if (defined(sitesOnlyVcfOutput) && select_first([sitesOnlyVcfOutput])) then "--sites-only-vcf-output" else ""} \
      ~{if (defined(tmpDir) && select_first([tmpDir])) then "--tmp-dir" else ""} \
      ~{if (defined(useJdkDeflater) && select_first([useJdkDeflater])) then "--use-jdk-deflater" else ""} \
      ~{if (defined(useJdkInflater) && select_first([useJdkInflater])) then "--use-jdk-inflater" else ""} \
      ~{if (defined(verbosity) && select_first([verbosity])) then "--verbosity" else ""} \
      ~{if (defined(version) && select_first([version])) then "--version" else ""} \
      ~{if (defined(disableToolDefaultReadFilters) && select_first([disableToolDefaultReadFilters])) then "--disable-tool-default-read-filters" else ""} \
      ~{if (defined(showhidden) && select_first([showhidden])) then "--showHidden" else ""} \
      ~{if defined(ambigFilterBases) then ("--ambig-filter-bases " + ambigFilterBases) else ''} \
      ~{if defined(ambigFilterFrac) then ("--ambig-filter-frac " + ambigFilterFrac) else ''} \
      ~{if (defined(maxFragmentLength) && select_first([maxFragmentLength])) then "--max-fragment-length" else ""} \
      ~{if (defined(minFragmentLength) && select_first([minFragmentLength])) then "--min-fragment-length" else ""} \
      ~{if defined(keepIntervals) then ("--keep-intervals '" + keepIntervals + "'") else ""} \
      ~{if defined(library) then ("--library '" + library + "'") else ""} \
      ~{if defined(maximumMappingQuality) then ("--maximum-mapping-quality " + maximumMappingQuality) else ''} \
      ~{if defined(minimumMappingQuality) then ("--minimum-mapping-quality " + minimumMappingQuality) else ''} \
      ~{if (defined(dontRequireSoftClipsBothEnds) && select_first([dontRequireSoftClipsBothEnds])) then "--dont-require-soft-clips-both-ends" else ""} \
      ~{if defined(filterTooShort) then ("--filter-too-short " + filterTooShort) else ''} \
      ~{if (defined(platformFilterName) && select_first([platformFilterName])) then "--platform-filter-name" else ""} \
      ~{if defined(blackListedLanes) then ("--black-listed-lanes '" + blackListedLanes + "'") else ""} \
      ~{if (defined(readGroupBlackList) && select_first([readGroupBlackList])) then "--read-group-black-list" else ""} \
      ~{if defined(keepReadGroup) then ("--keep-read-group '" + keepReadGroup + "'") else ""} \
      ~{if defined(maxReadLength) then ("--max-read-length " + maxReadLength) else ''} \
      ~{if defined(minReadLength) then ("--min-read-length " + minReadLength) else ''} \
      ~{if defined(readName) then ("--read-name '" + readName + "'") else ""} \
      ~{if (defined(keepReverseStrandOnly) && select_first([keepReverseStrandOnly])) then "--keep-reverse-strand-only" else ""} \
      ~{if defined(sample) then ("--sample '" + sample + "'") else ""} \
      ~{if (defined(invertSoftClipRatioFilter) && select_first([invertSoftClipRatioFilter])) then "--invert-soft-clip-ratio-filter" else ""} \
      ~{if defined(softClippedLeadingTrailingRatio) then ("--soft-clipped-leading-trailing-ratio " + softClippedLeadingTrailingRatio) else ''} \
      ~{if defined(softClippedRatioThreshold) then ("--soft-clipped-ratio-threshold " + softClippedRatioThreshold) else ''}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "broadinstitute/gatk:4.1.4.0"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "~{basename(variant, ".vcf.gz")}.filtered.vcf"])
    File out_tbi = select_first([outputFilename, "~{basename(variant, ".vcf.gz")}.filtered.vcf"]) + ".tbi"
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: VariantFiltration'
doc: |
  USAGE: VariantFiltration [arguments]
  Filter variant calls based on INFO and/or FORMAT annotations.
  Version:4.1.3.0

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: broadinstitute/gatk:4.1.4.0

inputs:
- id: javaOptions
  label: javaOptions
  type:
  - type: array
    items: string
  - 'null'
- id: compression_level
  label: compression_level
  doc: |-
    Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
  type:
  - int
  - 'null'
- id: outputFilename
  label: outputFilename
  doc: (-O) File to which variants should be written Required.
  type:
  - string
  - 'null'
  default: generated.filtered.vcf
  inputBinding:
    prefix: --output
    valueFrom: $(inputs.variant.basename.replace(/.vcf.gz$/, "")).filtered.vcf
    separate: true
- id: variant
  label: variant
  doc: (-V) A VCF file containing variants Required.
  type: File
  secondaryFiles:
  - pattern: .tbi
  inputBinding:
    prefix: --variant
    separate: true
- id: addOutputSamProgramRecord
  label: addOutputSamProgramRecord
  doc: |-
    (-add-output-sam-program-record)  If true, adds a PG tag to created SAM/BAM/CRAM files.  Default value: true. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --add-output-sam-program-record
    separate: true
- id: addOutputVcfCommandLine
  label: addOutputVcfCommandLine
  doc: |-
    (-add-output-vcf-command-line)  If true, adds a command line header line to created VCF files.  Default value: true. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --add-output-vcf-command-line
    separate: true
- id: arguments_file
  label: arguments_file
  doc: |-
    read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --arguments_file
    separate: true
- id: cloudIndexPrefetchBuffer
  label: cloudIndexPrefetchBuffer
  doc: |-
    (-CIPB)  Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.  Default value: -1.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cloud-index-prefetch-buffer
    separate: true
- id: cloudPrefetchBuffer
  label: cloudPrefetchBuffer
  doc: |-
    (-CPB)  Size of the cloud-only prefetch buffer (in MB; 0 to disable).  Default value: 40.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cloud-prefetch-buffer
    separate: true
- id: clusterSize
  label: clusterSize
  doc: |-
    (-cluster)  The number of SNPs which make up a cluster. Must be at least 2  Default value: 3.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cluster-size
    separate: true
- id: clusterWindowSize
  label: clusterWindowSize
  doc: |-
    (-window)  The window size (in bases) in which to evaluate clustered SNPs  Default value: 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --cluster-window-size
    separate: true
- id: createOutputBamIndex
  label: createOutputBamIndex
  doc: |-
    (-OBI)  If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.  Default value: true. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --create-output-bam-index
    separate: true
- id: createOutputBamMd5
  label: createOutputBamMd5
  doc: |-
    (-OBM)  If true, create a MD5 digest for any BAM/SAM/CRAM file created  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --create-output-bam-md5
    separate: true
- id: createOutputVariantIndex
  label: createOutputVariantIndex
  doc: |-
    (-OVI)  If true, create a VCF index when writing a coordinate-sorted VCF file.  Default value: true. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --create-output-variant-index
    separate: true
- id: createOutputVariantMd5
  label: createOutputVariantMd5
  doc: |-
    (-OVM)  If true, create a a MD5 digest any VCF file created.  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --create-output-variant-md5
    separate: true
- id: disableBamIndexCaching
  label: disableBamIndexCaching
  doc: |-
    (-DBIC)  If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified.  Caching is automatically disabled if there are no intervals specified.  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --disable-bam-index-caching
    separate: true
- id: disableReadFilter
  label: disableReadFilter
  doc: |-
    (-DF)  Read filters to be disabled before analysis  This argument may be specified 0 or more times. Default value: null. Possible Values: {WellformedReadFilter}
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --disable-read-filter
    separate: true
- id: disableSequenceDictionaryValidation
  label: disableSequenceDictionaryValidation
  doc: |-
    (-disable-sequence-dictionary-validation)  If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --disable-sequence-dictionary-validation
    separate: true
- id: excludeIntervals
  label: excludeIntervals
  doc: '(-XL) This argument may be specified 0 or more times. Default value: null. '
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --exclude-intervals
    separate: true
- id: filterExpression
  label: filterExpression
  doc: |-
    (-filter)  One or more expressions used with INFO fields to filter  This argument may be specified 0 or more times. Default value: null.
  type:
  - type: array
    inputBinding:
      prefix: --filter-expression
      separate: true
    items: string
  - 'null'
  inputBinding: {}
- id: filterName
  label: filterName
  doc: |-
    Names to use for the list of filters This argument may be specified 0 or more times. Default value: null.
  type:
    type: array
    inputBinding:
      prefix: --filter-name
      separate: true
    items:
    - string
    - 'null'
  inputBinding: {}
- id: filterNotInMask
  label: filterNotInMask
  doc: |-
    Filter records NOT in given input mask. Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --filter-not-in-mask
    separate: true
- id: gatkConfigFile
  label: gatkConfigFile
  doc: 'A configuration file to use with the GATK. Default value: null.'
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --gatk-config-file
    separate: true
- id: gcsMaxRetries
  label: gcsMaxRetries
  doc: |-
    (-gcs-retries)  If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection  Default value: 20.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --gcs-max-retries
    separate: true
- id: gcsProjectForRequesterPays
  label: gcsProjectForRequesterPays
  doc: |2-
     Project to bill when accessing 'requester pays' buckets. If unset, these buckets cannot be accessed.  Default value: .
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --gcs-project-for-requester-pays
    separate: true
- id: genotypeFilterExpression
  label: genotypeFilterExpression
  doc: |-
    (-G-filter)  One or more expressions used with FORMAT (sample/genotype-level) fields to filter (see documentation guide for more info)  This argument may be specified 0 or more times. Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --genotype-filter-expression
    separate: true
- id: genotypeFilterName
  label: genotypeFilterName
  doc: |-
    (-G-filter-name)  Names to use for the list of sample/genotype filters (must be a 1-to-1 mapping); this name is put in the FILTER field for variants that get filtered  This argument may be specified 0 or more times. Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --genotype-filter-name
    separate: true
- id: help
  label: help
  doc: |-
    (-h) display the help message Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --help
    separate: true
- id: inp
  label: inp
  doc: |-
    (-I) BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times. Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --input
    separate: true
- id: intervalExclusionPadding
  label: intervalExclusionPadding
  doc: |-
    (-ixp)  Amount of padding (in bp) to add to each interval you are excluding.  Default value: 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --interval-exclusion-padding
    separate: true
- id: intervalMergingRule
  label: intervalMergingRule
  doc: |-
    (-imr)  Interval merging rule for abutting intervals  Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --interval-merging-rule
    separate: true
- id: intervalPadding
  label: intervalPadding
  doc: '(-ip) Default value: 0.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --interval-padding
    separate: true
- id: intervalSetRule
  label: intervalSetRule
  doc: |-
    (-isr)  Set merging approach to use for combining interval inputs  Default value: UNION. Possible values: {UNION, INTERSECTION}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --interval-set-rule
    separate: true
- id: intervals
  label: intervals
  doc: |-
    (-L) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --intervals
    separate: true
- id: invalidatePreviousFilters
  label: invalidatePreviousFilters
  doc: |2-
     Remove previous filters applied to the VCF  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --invalidate-previous-filters
    separate: true
- id: invertFilterExpression
  label: invertFilterExpression
  doc: |-
    (-invfilter)  Invert the selection criteria for --filter-expression  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --invert-filter-expression
    separate: true
- id: invertGenotypeFilterExpression
  label: invertGenotypeFilterExpression
  doc: |-
    (-invG-filter)  Invert the selection criteria for --genotype-filter-expression  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --invert-genotype-filter-expression
    separate: true
- id: lenient
  label: lenient
  doc: |-
    (-LE) Lenient processing of VCF files Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --lenient
    separate: true
- id: mask
  label: mask
  doc: '(-mask) Input mask Default value: null.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --mask
    separate: true
- id: maskExtension
  label: maskExtension
  doc: |-
    How many bases beyond records from a provided 'mask' should variants be filtered Default value: 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --mask-extension
    separate: true
- id: maskName
  label: maskName
  doc: |-
    The text to put in the FILTER field if a 'mask' is provided and overlaps with a variant call  Default value: Mask.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --mask-name
    separate: true
- id: missingValuesEvaluateAsFailing
  label: missingValuesEvaluateAsFailing
  doc: |2-
     When evaluating the JEXL expressions, missing values should be considered failing the expression  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --missing-values-evaluate-as-failing
    separate: true
- id: quiet
  label: quiet
  doc: |-
    Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --QUIET
    separate: true
- id: readFilter
  label: readFilter
  doc: |-
    (-RF) Read filters to be applied before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter, AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator, FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter, MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter, MetricsReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter}
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --read-filter
    separate: true
- id: readIndex
  label: readIndex
  doc: |-
    (-read-index)  Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.  This argument may be specified 0 or more times. Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --read-index
    separate: true
- id: readValidationStringency
  label: readValidationStringency
  doc: |-
    (-VS)  Validation stringency for all SAM/BAM/CRAM/SRA files read by this program.  The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.  Default value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --read-validation-stringency
    separate: true
- id: reference
  label: reference
  doc: '(-R) Reference sequence Default value: null.'
  type:
  - File
  - 'null'
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
  inputBinding:
    prefix: --reference
    separate: true
- id: secondsBetweenProgressUpdates
  label: secondsBetweenProgressUpdates
  doc: |-
    (-seconds-between-progress-updates)  Output traversal statistics every time this many seconds elapse  Default value: 10.0.
  type:
  - double
  - 'null'
  inputBinding:
    prefix: --seconds-between-progress-updates
    separate: true
- id: sequenceDictionary
  label: sequenceDictionary
  doc: |-
    (-sequence-dictionary)  Use the given sequence dictionary as the master/canonical sequence dictionary.  Must be a .dict file.  Default value: null.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --sequence-dictionary
    separate: true
- id: setFilteredGenotypeToNoCall
  label: setFilteredGenotypeToNoCall
  doc: |2-
     Set filtered genotypes to no-call  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --set-filtered-genotype-to-no-call
    separate: true
- id: sitesOnlyVcfOutput
  label: sitesOnlyVcfOutput
  doc: |2-
     If true, don't emit genotype fields when writing vcf file output.  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --sites-only-vcf-output
    separate: true
- id: tmpDir
  label: tmpDir
  doc: 'Temp directory to use. Default value: null.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --tmp-dir
    separate: true
- id: useJdkDeflater
  label: useJdkDeflater
  doc: |-
    (-jdk-deflater)  Whether to use the JdkDeflater (as opposed to IntelDeflater)  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --use-jdk-deflater
    separate: true
- id: useJdkInflater
  label: useJdkInflater
  doc: |-
    (-jdk-inflater)  Whether to use the JdkInflater (as opposed to IntelInflater)  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --use-jdk-inflater
    separate: true
- id: verbosity
  label: verbosity
  doc: |-
    (-verbosity)  Control verbosity of logging.  Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --verbosity
    separate: true
- id: version
  label: version
  doc: |-
    display the version number for this tool Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --version
    separate: true
- id: disableToolDefaultReadFilters
  label: disableToolDefaultReadFilters
  doc: |-
    (-disable-tool-default-read-filters)  Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --disable-tool-default-read-filters
    separate: true
- id: showhidden
  label: showhidden
  doc: |-
    (-showHidden)  display hidden arguments  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --showHidden
    separate: true
- id: ambigFilterBases
  label: ambigFilterBases
  doc: |-
    Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction.  Default value: null.  Cannot be used in conjuction with argument(s) maxAmbiguousBaseFraction
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --ambig-filter-bases
    separate: true
- id: ambigFilterFrac
  label: ambigFilterFrac
  doc: |-
    Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases
  type:
  - double
  - 'null'
  inputBinding:
    prefix: --ambig-filter-frac
    separate: true
- id: maxFragmentLength
  label: maxFragmentLength
  doc: 'Default value: 1000000.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --max-fragment-length
    separate: true
- id: minFragmentLength
  label: minFragmentLength
  doc: 'Default value: 0.'
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --min-fragment-length
    separate: true
- id: keepIntervals
  label: keepIntervals
  doc: |-
    One or more genomic intervals to keep This argument must be specified at least once. Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --keep-intervals
    separate: true
- id: library
  label: library
  doc: |-
    (-library) Name of the library to keep This argument must be specified at least once. Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --library
    separate: true
- id: maximumMappingQuality
  label: maximumMappingQuality
  doc: ' Maximum mapping quality to keep (inclusive)  Default value: null. '
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --maximum-mapping-quality
    separate: true
- id: minimumMappingQuality
  label: minimumMappingQuality
  doc: ' Minimum mapping quality to keep (inclusive)  Default value: 10. '
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --minimum-mapping-quality
    separate: true
- id: dontRequireSoftClipsBothEnds
  label: dontRequireSoftClipsBothEnds
  doc: |2-
     Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --dont-require-soft-clips-both-ends
    separate: true
- id: filterTooShort
  label: filterTooShort
  doc: 'Minimum number of aligned bases Default value: 30.'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --filter-too-short
    separate: true
- id: platformFilterName
  label: platformFilterName
  doc: This argument must be specified at least once. Required.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --platform-filter-name
    separate: true
- id: blackListedLanes
  label: blackListedLanes
  doc: |-
    Platform unit (PU) to filter out This argument must be specified at least once. Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --black-listed-lanes
    separate: true
- id: readGroupBlackList
  label: readGroupBlackList
  doc: 'This argument must be specified at least once. Required. '
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --read-group-black-list
    separate: true
- id: keepReadGroup
  label: keepReadGroup
  doc: The name of the read group to keep Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --keep-read-group
    separate: true
- id: maxReadLength
  label: maxReadLength
  doc: Keep only reads with length at most equal to the specified value Required.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --max-read-length
    separate: true
- id: minReadLength
  label: minReadLength
  doc: |-
    Keep only reads with length at least equal to the specified value Default value: 1.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-read-length
    separate: true
- id: readName
  label: readName
  doc: Keep only reads with this read name Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --read-name
    separate: true
- id: keepReverseStrandOnly
  label: keepReverseStrandOnly
  doc: |2-
     Keep only reads on the reverse strand  Required. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --keep-reverse-strand-only
    separate: true
- id: sample
  label: sample
  doc: |-
    (-sample) The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --sample
    separate: true
- id: invertSoftClipRatioFilter
  label: invertSoftClipRatioFilter
  doc: |2-
     Inverts the results from this filter, causing all variants that would pass to fail and visa-versa.  Default value: false. Possible values: {true, false}
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --invert-soft-clip-ratio-filter
    separate: true
- id: softClippedLeadingTrailingRatio
  label: softClippedLeadingTrailingRatio
  doc: |2-
     Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered.  Default value: null.  Cannot be used in conjuction with argument(s) minimumSoftClippedRatio
  type:
  - double
  - 'null'
  inputBinding:
    prefix: --soft-clipped-leading-trailing-ratio
    separate: true
- id: softClippedRatioThreshold
  label: softClippedRatioThreshold
  doc: |2-
     Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered.  Default value: null.  Cannot be used in conjuction with argument(s) minimumLeadingTrailingSoftClippedRatio
  type:
  - double
  - 'null'
  inputBinding:
    prefix: --soft-clipped-ratio-threshold
    separate: true

outputs:
- id: out
  label: out
  type: File
  secondaryFiles:
  - pattern: .tbi
  outputBinding:
    glob: $(inputs.variant.basename.replace(/.vcf.gz$/, "")).filtered.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- gatk
- VariantFiltration
arguments:
- prefix: --java-options
  position: -1
  valueFrom: |-
    $("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 4].filter(function (inner) { return inner != null })[0] * 3) / 4)).replace(/\{compression\}/g, (inputs.compression_level != null) ? ("-Dsamjdk.compress_level=" + inputs.compression_level) : "").replace(/\{otherargs\}/g, [inputs.javaOptions, []].filter(function (inner) { return inner != null })[0].join(" ")))

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Gatk4Variantfiltration