@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 ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@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/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "vcf index" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl#indexed_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl#bgzipped_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#vcf> .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl#indexed_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl#file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bgzip VCF" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-c" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl#file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/bgzip.cwl#bgzipped_file> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:stdout               "$(inputs.file.basename).gz" .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "bgzip and index VCF" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#bgzip> , <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#indexed_vcf> .

<https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#indexed_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/9c9e6a6a48eb321804ce772a2c2c12b4f2f32529/definitions/subworkflows/bgzip_and_index.cwl#index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .