@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/nthreads>
        cwl:inputBinding  [ CommandLineBinding:position  10 ;
                            CommandLineBinding:prefix    "nthreads=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:default       16 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt>
        a                        cwl:CommandLineTool ;
        rdfs:label               "conform-gt" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     CommandLineBinding:prefix    "-jar" ;
                                     cwl:valueFrom                "/tools/conform-gt.24May16.cee.jar"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "match=" ;
                                     CommandLineBinding:separate  false ;
                                     cwl:valueFrom                "POS"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "java" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/region> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/outprefix> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/ref> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/log> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ghcr.io/ddbj/beagle-5.2:1.1.0"
                                 ] .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/vcf>
        cwl:format         <http://edamontology.org/format_3016> ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outprefix).vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/ref>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_vcf> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/region>
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "chrom=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/outprefix>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-prefix> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/ref>
        rdfs:comment      "Reference VCF file" ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "ref=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-log>
        cwl:outputSource  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/log> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation>
        a                        cwl:CommandLineTool ;
        rdfs:label               "beagle-imputation" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     CommandLineBinding:prefix    "-jar" ;
                                     cwl:valueFrom                "/usr/local/share/beagle-5.2_21Apr21.304-0/beagle.jar"
                                   ]
                                   [ CommandLineBinding:position  8 ;
                                     CommandLineBinding:prefix    "impute=" ;
                                     CommandLineBinding:separate  false ;
                                     cwl:valueFrom                "true"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "java" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/nthreads> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/java_options> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/outprefix> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/map> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/region> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/ref> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/gp> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/vcf> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/log> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ghcr.io/ddbj/beagle-5.2:1.1.0"
                                 ] .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_vcf>
        rdfs:comment  "Reference VCF file" ;
        sld:type      cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/gp>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gp> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/map>
        rdfs:comment  "Genetic map file" ;
        sld:type      cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/gp>
        cwl:inputBinding  [ CommandLineBinding:position  9 ;
                            CommandLineBinding:prefix    "gp=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:default       true ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/outprefix>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "out=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gt>
        rdfs:comment  "Target VCF file" ;
        sld:type      cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/ref>
        rdfs:comment      "Reference file" ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "ref=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/region>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/region> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-prefix>
        rdfs:comment  "Output prefix for conform-gt" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation>
        rdfs:label  "beagle-imputation" ;
        cwl:in      <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/nthreads> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/map> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/gp> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/region> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/ref> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/outprefix> ;
        cwl:out     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/log> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/vcf> ;
        cwl:run     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/gt>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gt> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-tbi>
        cwl:outputSource  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index/tbi> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/nthreads>
        rdfs:comment  "Number of threads" ;
        sld:default   16 ;
        sld:type      xsd:int .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/ref>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_bref3> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/region>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "chrom=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt>
        rdfs:label  "conform-gt" ;
        cwl:in      <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/outprefix> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/region> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/ref> ;
        cwl:out     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/log> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/vcf> ;
        cwl:run     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/gt>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/vcf> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl#bcftools-index-t>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bcftools-index-t" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(inputs.vcf.basename).tbi"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bcftools" "index" "-t" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl#bcftools-index-t/vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl#bcftools-index-t/tbi> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "biocontainers/bcftools:v1.9-1-deb_cv1"
                                 ] .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/map>
        rdfs:comment      "Genetic map file" ;
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "map=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/gt>
        rdfs:comment      "Target VCF file" ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "gt=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/gt>
        rdfs:comment      "Target VCF file" ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "gt=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-prefix>
        rdfs:comment  "Output prefix for beagle" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/region>
        rdfs:comment  "Target region (<chrom> or <chrom>:<start>-<end>)" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/nthreads>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/nthreads> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/log>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outprefix).log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/map>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/map> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl#bcftools-index-t/tbi>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename).tbi" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl#bcftools-index-t/vcf>
        rdfs:comment      "A VCF file containing variants" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index>
        rdfs:label  "beagle-vcf-index" ;
        cwl:in      <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index/vcf> ;
        cwl:out     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index/tbi> ;
        cwl:run     <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/bcftools-index-t.cwl> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation/vcf> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region>
        a                        cwl:Workflow ;
        rdfs:label               "beagle-imputation-per-region" ;
        ns1:original_cwlVersion  "v1.1" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-imputation> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf-index> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_bref3> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/region> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/map> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gt> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-prefix> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_vcf> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-prefix> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gp> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/nthreads> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-vcf> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-log> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-vcf> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/beagle-tbi> , <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-log> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-log>
        cwl:outputSource  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/log> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/outprefix>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt-prefix> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/log>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outprefix).log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/outprefix>
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "out=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/beagle-imputation.cwl#beagle-imputation/java_options>
        cwl:inputBinding  [ CommandLineBinding:position    1 ;
                            CommandLineBinding:shellQuote  false
                          ] ;
        sld:default       "-Xmx64g" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/conform-gt/region>
        cwl:source  <https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/region> .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Tools/conform-gt.cwl#conform-gt/vcf>
        cwl:format         <http://edamontology.org/format_3016> ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outprefix).vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/ref_bref3>
        rdfs:comment  "Reference file" ;
        sld:type      cwl:File .

<https://w3id.org/cwl/view/git/332d056002c06e65f0b1a454eb5cca2b2537db18/Workflows/beagle-imputation-per-region.cwl#beagle-imputation-per-region/gp>
        rdfs:comment  "A flag controling whether output genotype probability (true or false)" ;
        sld:default   true ;
        sld:type      xsd:string .