@prefix LoadListingRequirement: . @prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix rdfs: . @prefix ResourceRequirement: . @prefix CommandOutputBinding: . @prefix ns1: . cwl:source ; cwl:valueFrom "$(self).score.gz" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "dedup_pre.log" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "${ return self ? self.dedup_pre : []; }\n" . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "-d" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "tranches_file=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:default "Realigner" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--trim_soft_clip" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--after" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--after" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--after" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--traverse_param" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.metrics)" ] ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "${ return self + \".csv\"; }" . cwl:source ; cwl:valueFrom "${ return self ? self.bqsr : []; }\n" . sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:source . sld:type sld:null ; sld:type [ sld:fields , ; sld:type sld:record ] . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--metrics" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--interval" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--interval" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--interval" ] ; sld:type cwl:File , xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:fields , ; sld:type sld:record ] . cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:default "LocusCollector" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; sld:type xsd:string . cwl:in , , , , , , ; cwl:out ; cwl:run . sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . sld:type xsd:string . sld:type xsd:int , sld:null . sld:type xsd:string . cwl:source ; cwl:valueFrom "${ return self + \".pdf\"; }" . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-q" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-q" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-q" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "qd=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 150 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--pcr_indel_model" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:stderr "dedup.log" . cwl:outputBinding [ CommandOutputBinding:glob "plot.log" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sentieon" "plot" ) ; 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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ] ; cwl:stderr "plot.log" . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--traverse_param" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "isize=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . a cwl:Workflow ; rdfs:comment "run 2-pass dedup: algo LocusCollector + algo Dedup sequentially" ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--gq_bands" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:stderr "hc.log" . cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . a cwl:Workflow ; rdfs:comment "Run BQSR pre+post+plot flow" ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--rmdup" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "bqsr.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "bqsr.log" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--plot" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--plot" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--plot" ] ; sld:type xsd:boolean , sld:null . cwl:valueFrom "${ return true; }" . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--merge" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--merge" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--merge" ] ; sld:type xsd:boolean , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "${ return self ? self.dedup : []; }\n" . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--annotation" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 20 ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 180 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 150 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--min_base_qual" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "gc=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . sld:type cwl:File , xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--traverse_param" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--traverse_param" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "target_titv=" ; CommandLineBinding:separate false ] ; sld:type xsd:double , sld:null . cwl:source . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source , ; cwl:valueFrom "${\n if(self[1] != null)\n return self[1];\n else\n return self[0] + \".csv\";\n} \n" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:baseCommand ( "sentieon" "driver" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "bqsr.log" . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--phasing" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File , xsd:string , sld:null . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--merge" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source , ; cwl:valueFrom "${\n if(self[1] != null)\n return self[1];\n else\n return self[0] + \".pdf\";\n} \n" . cwl:default "Haplotyper" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; sld:type xsd:string . cwl:default "score_info" ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--fun" ] ; sld:type xsd:string . cwl:valueFrom "${ return \"bqsr\"; }" . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--dup_read_name" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--emit_conf" ] ; sld:type xsd:double , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "min_fp_rate=" ; CommandLineBinding:separate false ] ; sld:type xsd:double , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--interval_list" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--before" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--before" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--before" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "hc.log" ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:default "QualCal" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 150 ] ; sld:type xsd:string . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--interval" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "-d" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . a cwl:Workflow ; rdfs:comment "DNAseq pipeline from bam to vcf" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.threads)" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "dedup_pre.log" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "realign.log" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--prune_factor" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 180 ] ; sld:type sld:null ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--score_info" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--output_dup_read_name" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:inputBinding [ CommandLineBinding:position 110 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--merge" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--optical_dup_pix_dist" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:source ; cwl:valueFrom "${ return self ? self.bqsr_post : []; }\n" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 110 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "dedup.log" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 180 ] ; cwl:inputBinding [ CommandLineBinding:position 180 ] ; cwl:inputBinding [ CommandLineBinding:position 180 ] ; sld:type sld:null ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 150 ] ; cwl:inputBinding [ CommandLineBinding:position 150 ] ; cwl:inputBinding [ CommandLineBinding:position 150 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--bam_compression" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--qcal" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--qcal" ] ; cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--qcal" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-q" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sentieon" "driver" ) ; 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 "$(inputs.threads)" ] ; cwl:stderr "realign.log" . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--interval" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--emit_mode" ] ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self).post" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-t" ] ; sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--shard" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 150 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--call_conf" ] ; sld:type xsd:double , sld:null . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "mq=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:source . cwl:default "Dedup" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--algo" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 10 ] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:items cwl:File , xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 110 ; CommandLineBinding:prefix "--ploidy" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 50 ; CommandLineBinding:prefix "point_size=" ; CommandLineBinding:separate false ] ; sld:type xsd:double , sld:null . cwl:source .