@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: .
cwl:source .
rdfs:comment "vcf file" ;
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type cwl:File .
sld:type cwl:File .
rdfs:comment "window size" ;
cwl:default 250 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--snp_nbhd" ] ;
sld:type xsd:int , sld:null .
cwl:valueFrom "${ return inputs.normal_bam.basename.replace(\".bam\", \"\") + \"__\" + inputs.tumor_bam.basename.replace(\".bam\", \"\") + \".dat.gz\"; }" .
rdfs:comment "normal bam" ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type cwl:File .
rdfs:comment "critical value for segmentation" ;
cwl:default 500 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--purity_cval" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "critical value for segmentation" ;
cwl:default 100 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--cval" ] ;
sld:type xsd:int , sld:null .
cwl:source .
sld:type xsd:string .
rdfs:comment "Sets the maximum depth. Default is 4000." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--max-depth" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "output prefix" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--directory" ] ;
sld:type xsd:string .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs , , , , , , ;
cwl:requirements [ a cwl:ScatterFeatureRequirement ] ;
cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:default "50" .
cwl:source .
rdfs:comment "Perform analysis on single chromosome" ;
cwl:default "F" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--single_chrom" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:File .
rdfs:comment "Show detailed messages." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--verbose" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "Plots using ggplot2" ;
cwl:default "T" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ggplot2" ] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:valueFrom "${ return true; }" .
rdfs:comment "threshold for depth in the normal sample" ;
cwl:default 35 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--ndepth" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:int .
sld:type xsd:int .
a cwl:CommandLineTool ;
rdfs:comment "run snp-pileup\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "/usr/bin/snp-pileup" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 8000
] ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-htstools:0.1.1"
] .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "Which version of FACETs to load into R" ;
cwl:default "latest" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--R_lib" ] ;
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"*.seg" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
rdfs:comment "paired Counts File" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--counts_file" ] ;
sld:type cwl:File .
cwl:valueFrom "${ return inputs.counts_file.basename.replace(\".dat.gz\", \"\"); }" .
rdfs:comment "Genome of counts file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--genome" ] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
a cwl:CommandLineTool ;
rdfs:comment "Run FACETS on tumor-normal SNP read counts generated using cmo_snp-pileup\n" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "python" "/usr/bin/facets-suite/facets" "doFacets" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , , , , , ;
cwl:outputs , , , , , ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mskcc/roslin-variant-facets:1.6.3"
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 8000
] .
rdfs:comment "minimum number of heterozygote snps in a segment used for bivariate t-statistic during clustering of segments" ;
cwl:default 25 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--purity_min_nhet" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "output file" ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"*.Rdata" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*_purity.cncf.txt" ] ;
sld:type cwl:File .
rdfs:comment "log stdout to file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--stdout" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "tumor bam" ;
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
rdfs:comment "Compresses the output file with BGZF." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--gzip" ] ;
sld:type xsd:boolean , sld:null .
rdfs:comment "log stderr to file" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--stderr" ] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , , , , , , ;
cwl:out , , , , , ;
cwl:run .
rdfs:comment "Every MULTIPLE positions, if there is no SNP,insert a blank record with the total count at theposition." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--pseudo-snps" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "output prefix" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--TAG" ] ;
sld:type xsd:string .
rdfs:comment "diploid log ratio" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--dipLogR" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "window size" ;
cwl:default 250 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--purity_snp_nbhd" ] ;
sld:type xsd:int , sld:null .
cwl:valueFrom "${ return true; }" .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:default "hg19" .
cwl:outputBinding [ CommandOutputBinding:glob
"*.out" ] ;
sld:type [ sld:items cwl:File ;
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 .
cwl:outputBinding [ CommandOutputBinding:glob
"*.png" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"*_hisens.cncf.txt" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"${\n if (inputs.output_file)\n return inputs.output_file;\n return null;\n}\n" ] ;
sld:type cwl:File .
rdfs:comment "Sets the minimum threshold for base quality.Default is 0." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min-base-quality" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Set the value for tumor id" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--tumor_id" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Comma separated list of minimum read counts fora position to be output. Default is 0." ;
cwl:default "10,0" ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min-read-counts" ] ;
sld:type xsd:string , sld:null .
rdfs:comment "Set the seed for reproducibility" ;
cwl:default 1000 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--seed" ] ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:comment "Do not discard anomalous read pairs." ;
cwl:default false ;
cwl:inputBinding [ CommandLineBinding:prefix
"--count-orphans" ] ;
sld:type xsd:boolean , sld:null .
cwl:default "." .
rdfs:comment "threshold for depth in the normal sample" ;
cwl:default 35 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--purity_ndepth" ] ;
sld:type xsd:int , sld:null .
cwl:source .
sld:type xsd:string .
rdfs:comment "minimum number of heterozygote snps in a segment used for bivariate t-statistic during clustering of segments" ;
cwl:default 25 ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min_nhet" ] ;
sld:type xsd:int , sld:null .
rdfs:comment "Sets the minimum threshold for mappingquality. Default is 0." ;
cwl:inputBinding [ CommandLineBinding:prefix
"--min-map-quality" ] ;
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:in , , , , , , ;
cwl:out ;
cwl:run .