@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
@prefix CommandLineTool: .
@prefix ExpressionTool: .
rdfs:comment "Power threshold for normal to determine germline vs variant" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--somatic_classification_normal_power_threshold"
] ;
sld:type xsd:boolean , sld:null .
sld:type cwl:File .
rdfs:comment "Tumor Bam file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tumor-bam" ] ;
sld:type cwl:File .
rdfs:comment "Arbitrary tag string to identify this GATK run as part of a group of runs, for later analysis" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tag"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "write out power in WIGGLE format to this file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--power_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-q"
] ;
sld:type xsd:float , sld:null .
rdfs:comment "Reference genome in fasta format" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--refFasta" ] ;
sld:type cwl:File , xsd:string .
sld:type xsd:string , sld:null .
rdfs:comment "The column for gene name, or segment annotation" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-g"
] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "Tumor sample ID" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tumor-id" ] ;
sld:type xsd:string , sld:null .
cwl:in , , , , ;
cwl:out ;
cwl:run .
rdfs:comment "Alias for -d none" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--remove-duplicates" ] ;
sld:type xsd:boolean , sld:null .
cwl:valueFrom "${ return true; }" .
cwl:source .
rdfs:comment "First coordinate of the next file can precede last record of the current file." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--rename-chrs" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "column number for region start [4]" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--begin" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Pedigree string for samples" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--pedigreeString"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "print only the header lines" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--only-header" ] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string , sld:null .
rdfs:comment "The number of nucleotide to extend for each segment, default - 0 -y" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-x"
] ;
sld:type xsd:string , sld:null .
sld:type xsd:string , sld:null .
cwl:source .
cwl:in , , , , , , ;
cwl:out ;
cwl:run .
cwl:source .
rdfs:comment "If set, reads with mapping quality less than INT will be filtered and ignored" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-Q"
] ;
sld:type xsd:string , sld:null .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:source .
rdfs:comment "exclude sites for which the expression is true (see man page for details)" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--exclude" ] ;
sld:type xsd:string , sld:null .
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
rdfs:comment "Tumor total depth threshold" ;
cwl:default 5 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--totaldepth" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "LOD threshold for calling normal non-variant at dbsnp sites" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--dbsnp_normal_lod"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Tumor variant frequency threshold" ;
cwl:default 1e-02 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--variantfraction" ] ;
sld:type xsd:float , 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 [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
rdfs:comment "Type of BAQ calculation to apply in the engine (OFF|CALCULATE_AS_NECESSARY| RECALCULATE)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--baq"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Tumor bam" ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "do not append version and command line to the header" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--no-version" ] ;
sld:type xsd:boolean , sld:null .
cwl:source .
sld:type [ sld:items xsd:string ;
sld:type sld:array
] ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"${ return inputs.vcf; }" ] ;
sld:type cwl:File .
cwl:in , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.vcf)\n return inputs.vcf;\n return null;\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "The column for segment starts in the region, e.g. exon starts" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-s"
] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "for computational efficiency, reject sites with allelic fraction below this threshold" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tumor_f_pretest"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "write out normal read depth in WIGGLE format to this file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--normal_depth_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details" ;
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:prefix "--columns"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default "5" .
rdfs:comment "Vcf file to be annotated" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
cwl:valueFrom "${ return inputs.b.basename.replace(\".bam\", \".\") + inputs.b2.basename.replace(\".bam\", \".vardict.vcf\") }" .
rdfs:comment "BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--baqGapOpenPenalty"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default "4" .
cwl:source .
rdfs:comment "SAM or BAM file(s)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--input_file:tumor"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File , sld:null .
rdfs:comment "Normal Sample Name" ;
sld:type xsd:string , sld:null .
cwl:in ;
cwl:out ;
cwl:run .
sld:type xsd:string , sld:null .
cwl:default false .
rdfs:comment "If provided, that GATK will stop execution cleanly as soon after maxRuntime has been exceeded, truncating the run but not exiting with a failure. By default the value is interpreted in minutes, but this can be changed by maxRuntimeUnits" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--maxRuntime"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
sld:type xsd:string .
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "name to use for tumor in output files" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--tumor_sample_name"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default "1" .
cwl:outputSource ;
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type xsd:string .
rdfs:comment "threshold for determining if there is relatedness between the alt and ref allele read piles" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--fraction_mapq0_threshold"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
rdfs:comment "The regular expression to extract sample name from bam filenames. Default to - /([^\\/\\._]+?)_[^\\/]*.bam/" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-n"
] ;
sld:type xsd:string , sld:null .
cwl:source .
rdfs:comment "How many CPU threads should be allocated per data thread to running this analysis?" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--num_cpu_threads_per_data_thread"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--intervals"
] ;
sld:type cwl:File , xsd:string , sld:null .
cwl:default "2" .
rdfs:comment "Indicates the interval merging rule we should use for abutting intervals (ALL| OVERLAPPING_ONLY)" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--interval_merging"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Show a progress bar. WARNING - requires additionaltime to calculate number of SNPs, and will takelonger than normal." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--progress" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "If set, reads with mapping quality less than INT will be filtered and ignored" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-Q"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Name of the tumor Sample" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tsampleName" ] ;
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-G"
] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "Ligate phased VCFs by matching phase at overlapping haplotypes" ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ligate" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "The total number of BAM file handles to keep open simultaneously" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--num_bam_file_handles"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--enable_extended_output"
] ;
sld:type xsd:boolean .
rdfs:comment "Pedigree files for samples" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--pedigree"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Maximum allowed tumor noise" ;
cwl:default 2e-01 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tum-noise" ] ;
sld:type xsd:float , sld:null .
rdfs:comment "Tumor allele depth threshold" ;
cwl:default 3 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--alleledepth" ] ;
sld:type xsd:int , sld:null .
rdfs:comment " b - compressed BCF, u - uncompressed BCF, z - compressed VCF, v - uncompressed VCF [v]" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--output-type" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Extension of bp to look for mismatches after insersion or deletion. Default to 3 bp, or only calls when they're within 3 bp." ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-X"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Compresses the output file with BGZF." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gzip" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "column number for sequence names (suppressed by -p) [1]" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--sequence" ] ;
sld:type xsd:string , sld:null .
cwl:valueFrom "${ return inputs.inputVcf.basename.replace(\".vcf\", \".complex_filtered.vcf\"); }" .
cwl:secondaryFiles [] ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
rdfs:comment "Input vcf muTect file which needs to be filtered" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--inputVcf" ] ;
sld:type cwl:File , xsd:string .
rdfs:comment "Output splicing read counts" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-i"
] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "list chromosome names" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--list-chroms" ] ;
sld:type xsd:boolean , sld:null .
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
rdfs:comment "write out 20x of Q20 coverage in WIGGLE format to this file" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--coverage_20_q20_file"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
rdfs:comment "Allelic fraction constant to use in power calculations" ;
cwl:inputBinding [ CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--power_constant_af"
] ;
sld:type sld:null ;
sld:type [ sld:items xsd:string ;
sld:type sld:array
] .
cwl:source .
sld:type cwl:File .
sld:type xsd:string , sld:null .
rdfs:comment "The minimum" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-B"
] ;
sld:type xsd:int , sld:null .
sld:type cwl:File .
sld:type xsd:string , sld:null .
rdfs:comment "Indicate wehther is zero-based cooridates, as IGV does. Default - 1 for BED file or amplicon BED file. Use 0 to turn it off. When use -R option, it's set to 0AUTHOR. Written by Zhongwu Lai, AstraZeneca, Boston, USAREPORTING BUGS. Report bugs to zhongwu@yahoo.comCOPYRIGHT. This is free software - you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law." ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-z"
] ;
sld:type xsd:string , sld:null .
rdfs:comment "Disable read-pair overlap detection." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ignore-overlaps" ] ;
sld:type xsd:boolean , sld:null .
cwl:source .
rdfs:comment "Full Path to the output dir." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--outDir" ] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
cwl:secondaryFiles [] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
rdfs:comment "The column for region start, e.g. gene start" ;
cwl:inputBinding [ CommandLineBinding:position 0 ;
CommandLineBinding:prefix "-S"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:source .
sld:type xsd:boolean , sld:null .
a cwl:CommandLineTool ;
rdfs:comment "Index vcf files\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/usr/local/bin/tabix" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , ,