@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix EnvVarRequirement: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns2: . @prefix SoftwarePackage: . @prefix ns1: . @prefix NetworkAccess: . @prefix SoftwareRequirement: . @prefix rdf: . @prefix EnvironmentDef: . @prefix cwl: . @prefix ResourceRequirement: . @prefix ExpressionTool: . cwl:in , , , , , , , , ; cwl:out ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 12288 ] ; cwl:run . cwl:source . rdfs:comment "The output tranches file used by ApplyRecalibration in SNP mode" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "the recal File" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_recal)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-tranchesFile" ] ; sld:type xsd:string . rdfs:comment "Heterozygosity for indel calling" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--heterozygosity" ] ; sld:type xsd:double , sld:null . rdfs:comment "multithreading option" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-nt" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-nt" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-Djava.io.tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-T" ; cwl:valueFrom "ApplyRecalibration" ] ) ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-Djava.io.tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-T" ; cwl:valueFrom "ApplyRecalibration" ] ) ; cwl:baseCommand ( "java" ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ ns2:citation "https://dx.doi.org/10.1038/ng.806" ; SoftwarePackage:package "gatk" ; SoftwarePackage:version "3.8" ] ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ ns2:citation "https://dx.doi.org/10.1038/ng.806" ; SoftwarePackage:package "gatk" ; SoftwarePackage:version "3.8" ] ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/gatk-base:3" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/gatk-base:3" ] . sld:fields , , ; sld:type sld:record . cwl:source . rdfs:comment "The output recal file used by ApplyRecalibration in INDEL mode" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "reference genome" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . rdfs:comment "1000 genome reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:1000G,known=false,training=true,truth=false,prior=10.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_GenotypeGVCFs)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Input prior for calls" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--input_prior" ] ; sld:type sld:null ; sld:type [ sld:items xsd:double ; sld:type sld:array ] . cwl:default 9.9e+01 . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-recalFile" ] ; sld:type xsd:string . rdfs:comment "Use additional trigger on variants found in an external alleles file" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sample_ploidy" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "One or more genomic intervals over which to operate" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--intervals" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--intervals" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "reference genome" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Maximum number of different clusters (gaussians) of variants the program is allowed to try to identify." ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--maxGaussians" ] ; sld:type xsd:int , sld:null . rdfs:comment "input vcf File raw variant calls from haplotype caller" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-input" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "dbSNP reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:string . a cwl:ExpressionTool ; rdfs:comment "The InbreedingCoeff is a population level statistic that requires at least 10 samples in order to be computed. For projects with fewer samples, or that includes many closely related samples (such as a family) please omit this annotation from the command line. From https://software.broadinstitute.org/gatk/documentation/article?id=1259\n" ; rdfs:label "Given an ExomeseqStudyType returns an array of the annotations to use." ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var annotations = inputs.base_annotations;\n var inputStudyType = inputs.study_type;\n if(inputStudyType === \"Large Population\") {\n annotations.push(\"InbreedingCoeff\");\n }\n return {\"annotations\": annotations };\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:default "-Xmx8g" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-jar" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-rscriptFile" ] ; sld:type xsd:string , sld:null . rdfs:comment "The output recalibration VCF file" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_recalibrated_vcf)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_recalibrated_vcf)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "latest_dbsnp.vcf set of known indels" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--dbsnp" ] ; sld:type cwl:File , sld:null . rdfs:comment "One or more classes/groups of annotations to apply to variant calls" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--group" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "One or more genomic intervals over which to operate" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--intervals" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "One or more genomic intervals over which to operate" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--intervals" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Amount of padding (in bp) to add to each interval" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--interval_padding" ] ; sld:type xsd:int , sld:null . rdfs:comment "The output recalibration R script for the plots" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_rscript)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "One or more input gVCF files" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-V" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:default 1 . sld:type . rdfs:comment "the tranches File" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_tranches)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "The output filtered and recalibrated VCF file in in which each variant is annotated with its VQSLOD value" ; cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "-Xmx8g" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-tranchesFile" ] ; sld:type xsd:string . cwl:source . rdfs:comment "Maximum number of PL values to output" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max_num_PL_values" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "Maximum number of genotypes to consider at any site" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max_genotype_count" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:default 1 . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-jar" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-jar" ] ; sld:type cwl:File . rdfs:comment "If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--annotateNDA" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "The output recalibration R script for the plots" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_rscript)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:source . cwl:source . rdfs:comment "Number of data threads to allocate to this analysis" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-nt" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:default "-Xmx4g" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type xsd:string . sld:type xsd:string . rdfs:label "The type of study" ; sld:symbols , ; sld:type sld:enum . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . rdfs:comment "Reference genome assembly, indexed" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "Include loci found to be non-variant after genotyping" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--includeNonVariantSites" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:int , sld:null . rdfs:comment "specify if VQSR is called on SNPs or Indels" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-mode" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string . cwl:source . rdfs:comment "Number of data threads to allocate to this analysis" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-nt" ] ; sld:type xsd:int , sld:null . rdfs:comment "Use new AF model instead of the so-called exact model" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--useNewAFCalculator" ] ; sld:type xsd:boolean , sld:null . cwl:default "INDEL" . rdfs:comment "VCF file from joint genotyping calling" ; cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "The output recal file used by ApplyRecalibration in SNP mode" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "One or more genomic intervals over which to operate" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--intervals" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . rdfs:comment "One or more specific annotations to apply to variant calls" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--annotation" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:default 1 . rdfs:comment "the recal file generated by VariantRecalibrator" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-recalFile" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-recalFile" ] ; sld:type cwl:File . rdfs:comment "Maximum number of different clusters (gaussians) of variants the program is allowed to try to identify." ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--maxGaussians" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type . cwl:source . cwl:default "FS" , "MQ" , "MQRankSum" , "QD" , "ReadPosRankSum" . cwl:source . a cwl:CommandLineTool ; rdfs:comment "GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n -jar gatk.jar\n -T VariantRecalibrator \\\n -R [reference_fasta] \\\n -recalFile $tmpDir/out.recal \\\n -tranchesFile $tmpDir/out.tranches \\\n -rscriptFile $tmpDir/out.R \\\n -nt 4 \\\n -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n -mode SNP \\\n -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \\\n -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \\\n -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-Djava.io.tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-T" ; cwl:valueFrom "VariantRecalibrator" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-mode" ; cwl:valueFrom "INDEL" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ ns2:citation "https://dx.doi.org/10.1038/ng.806" ; SoftwarePackage:package "gatk" ; SoftwarePackage:version "3.8" ] ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/gatk-base:3" ] . sld:type cwl:File . rdfs:comment "the tranches file generated by VariantRecalibrator" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-tranchesFile" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-tranchesFile" ] ; sld:type cwl:File . cwl:default "FS" , "MQ" , "MQRankSum" , "QD" , "ReadPosRankSum" , "SOR" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . rdfs:comment "omni reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:omni,known=false,training=true,truth=false,prior=12.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "name of the output file from GenotypeGVCFs" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . rdfs:comment "the tranches File" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_tranches)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-jar" ] ; sld:type cwl:File . cwl:default "-Xmx8g" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type xsd:string . sld:type xsd:string . rdfs:comment "reference genome" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , . cwl:source . rdfs:comment "the recal File" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputfile_recal)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "SNP" . rdfs:comment "hapmap reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:mills,known=false,training=true,truth=true,prior=12.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Heterozygosity for indel calling" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--indel_heterozygosity" ] ; sld:type xsd:double , sld:null . rdfs:comment "hapmap reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:hapmap,known=false,training=true,truth=true,prior=15.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:ExpressionTool ; rdfs:label "Generates a set of file names for joint steps based on an input name" ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n function makeFilename(base, suffix, extension) {\n return base + '-' + suffix + '.' + extension;\n }\n var base = inputs.name\n\n return {\n joint_genotype_raw_variants_output_filename: makeFilename(base, 'raw_variants', 'g.vcf'),\n snps_vqsr_recal_output_filename: makeFilename(base, 'snps_vqsr_recal', 'out'),\n snps_vqsr_tranches_output_filename: makeFilename(base, 'snps_vqsr_tranches', 'out'),\n snps_vqsr_rscript_output_filename: makeFilename(base, 'snps_vqsr', 'R'),\n snps_recalibrated_output_filename: makeFilename(base, 'snps_recalibrated', 'vcf'),\n snps_indels_vqsr_recal_output_filename: makeFilename(base, 'snps_indels_vqsr_recal', 'out'),\n snps_indels_vqsr_tranches_output_filename: makeFilename(base, 'snps_indels_vqsr_tranches', 'out'),\n snps_indels_vqsr_rscript_output_filename: makeFilename(base, 'snps_indels_vqsr', 'R'),\n snps_indels_recalibrated_output_filename: makeFilename(base, 'snps_indels_recalibrated', 'vcf')\n };\n}\n" ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in ; cwl:out , , , , , , , , ; cwl:run . rdfs:comment "The raw input variants to be recalibrated" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-input" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:default 9.9e+01 . cwl:source . sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-jar" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . a cwl:EnvVarRequirement ; EnvVarRequirement:envDef [ EnvironmentDef:envName "PATH" ; EnvironmentDef:envValue "/usr/local/bin/:/usr/bin:/bin" ] ; EnvVarRequirement:envDef [ EnvironmentDef:envName "PATH" ; EnvironmentDef:envValue "/usr/local/bin/:/usr/bin:/bin" ] ; EnvVarRequirement:envDef [ EnvironmentDef:envName "PATH" ; EnvironmentDef:envValue "/usr/local/bin/:/usr/bin:/bin" ] ; EnvVarRequirement:envDef [ EnvironmentDef:envName "PATH" ; EnvironmentDef:envValue "/usr/local/bin/:/usr/bin:/bin" ] ; EnvVarRequirement:envDef [ EnvironmentDef:envName "PATH" ; EnvironmentDef:envValue "/usr/local/bin/:/usr/bin:/bin" ] . rdfs:comment "The output rscript file generated by the VQSR in INDEL mode to aid in visualization of the input data and learned model" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "input vcf File raw variant calls from haplotype caller" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-input" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "dbSNP reference data" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-resource:dbsnp,known=true,training=false,truth=false,prior=2.0" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "StandardAnnotation" . rdfs:comment "filtering level default value is 99.9" ; cwl:default 9.99e+01 ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--ts_filter_level" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--ts_filter_level" ] ; sld:type xsd:float . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-rscriptFile" ] ; sld:type xsd:string , sld:null . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements . rdfs:comment "The names of the annotations which should used for calculations" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-an" ] ; sld:items xsd:string ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:int , sld:null . rdfs:comment "The output filtered and recalibrated VCF file in SNP mode in which each variant is annotated with its VQSLOD value" ; cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:comment "GATK-VariantsRecalibrator.cwl is developed for CWL consortium\n\nUsage:\n```\njava -Xmx8G \\\n -jar gatk.jar\n -T VariantRecalibrator \\\n -R [reference_fasta] \\\n -recalFile $tmpDir/out.recal \\\n -tranchesFile $tmpDir/out.tranches \\\n -rscriptFile $tmpDir/out.R \\\n -nt 4 \\\n -an MQRankSum -an ReadPosRankSum -an DP -an FS -an QD \\\n -mode SNP \\\n -resource:hapmap,known=false,training=true,truth=true,prior=15.0 [hapmap_vcf] \\\n -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 [dbsnp_vcf] \\\n -resource:omni,known=false,training=true,truth=true,prior=12.0 [1komni_vcf] \\\n -resource:1000G,known=false,training=true,truth=false,prior=10.0 [1ksnp_vcf]\n```\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-Djava.io.tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-T" ; cwl:valueFrom "VariantRecalibrator" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-mode" ; cwl:valueFrom "SNP" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ ns2:citation "https://dx.doi.org/10.1038/ng.806" ; SoftwarePackage:package "gatk" ; SoftwarePackage:version "3.8" ] ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/gatk-base:3" ] . cwl:source . cwl:source . rdfs:comment "Number of data threads to allocate to this analysis" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-nt" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-recalFile" ] ; sld:type xsd:string . sld:type cwl:File . rdfs:comment "The output rscript file generated by the VQSR in SNP mode to aid in visualization of the input data and learned model" ; cwl:outputSource ; sld:type cwl:File . rdfs:comment "The names of the annotations which should used for calculations" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-an" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:comment "The output tranches file used by ApplyRecalibration in INDEL mode" ; cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "The minimum phred-scaled confidence threshold at which variants should be called" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--standard_min_confidence_threshold_for_calling" ] ; sld:type xsd:double , sld:null . sld:type cwl:File . cwl:source . sld:type xsd:string . rdfs:comment "Heterozygosity for indel calling" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--heterozygosity_stdev" ] ; sld:type xsd:double , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "GATK-GenotypeGVCFs.cwl is developed for CWL consortium\nPerform joint genotyping on gVCF files produced by HaplotypeCaller\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-Djava.io.tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-T" ; cwl:valueFrom "GenotypeGVCFs" ] ) ; cwl:baseCommand ( "java" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ ns2:citation "https://dx.doi.org/10.1038/ng.806" ; SoftwarePackage:package "gatk" ; SoftwarePackage:version "3.8" ] ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "dukegcb/gatk-base:3" ] . rdfs:comment "Maximum number of alternate alleles to genotype" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max_alternate_alleles" ] ; sld:type xsd:int , sld:null .