@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix EnvVarRequirement: <https://w3id.org/cwl/cwl#EnvVarRequirement/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@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#> .
@prefix SecondaryFileSchema: <https://w3id.org/cwl/cwl#SecondaryFileSchema/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix EnvironmentDef: <https://w3id.org/cwl/cwl#EnvironmentDef/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/cram>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/cram> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/vcf>
        cwl:format         <http://edamontology.org/format_3016> ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).gridss.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/cram>
        cwl:format          <http://edamontology.org/format_3462> ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".crai" ] ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline-log>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/log> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/num_threads>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/num_threads> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/cram2bam_log>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/log> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/java_tool_options>
        sld:default  "" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/log>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cram.nameroot).bam.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/reference>
        rdfs:comment        "FastA file for reference genome" ;
        cwl:format          <http://edamontology.org/format_1929> ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".amb" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".bwt" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".pac" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".ann" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".fai" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".sa" ] ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam>
        rdfs:label  "samtools-cram2bam" ;
        cwl:in      <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/num_threads> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/reference> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/cram> ;
        cwl:out     <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/bam> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/log> ;
        cwl:run     <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/reference>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/reference> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gridss-germline" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:baseCommand          ( "bash" "/tools/gridss-germline.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/num_threads> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/java_tool_options> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/bam> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/reference> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/jvm_heap> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/log> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/idx> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/vcf> ;
        cwl:requirements         [ a                         cwl:EnvVarRequirement ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "NUM_THREADS" ;
                                                               EnvironmentDef:envValue  "$(inputs.num_threads)"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "VCF" ;
                                                               EnvironmentDef:envValue  "$(inputs.bam.nameroot).gridss.vcf"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "ASSEMBLY" ;
                                                               EnvironmentDef:envValue  "$(inputs.bam.nameroot).assembly.bam"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "JVM_HEAP" ;
                                                               EnvironmentDef:envValue  "$(inputs.jvm_heap)"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "JAVA_TOOL_OPTIONS" ;
                                                               EnvironmentDef:envValue  "$(inputs.java_tool_options)"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "REFERENCE" ;
                                                               EnvironmentDef:envValue  "$(inputs.reference.path)"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "GRIDSS_JAR" ;
                                                               EnvironmentDef:envValue  "/opt/gridss/gridss-2.9.4-gridss-jar-with-dependencies.jar"
                                                             ] ;
                                   EnvVarRequirement:envDef  [ EnvironmentDef:envName   "BAM" ;
                                                               EnvironmentDef:envValue  "$(inputs.bam.path)"
                                                             ]
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ghcr.io/ddbj/jga-analysis/gridss:1.0.0"
                                 ] ;
        cwl:stderr               "$(inputs.bam.nameroot).gridss.vcf.log" .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline>
        rdfs:label  "gridss-germline" ;
        cwl:in      <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/java_tool_options> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/reference> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/bam> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/jvm_heap> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/num_threads> ;
        cwl:out     <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/vcf> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/log> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/idx> ;
        cwl:run     <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/bam>
        cwl:format  <http://edamontology.org/format_2572> ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/jvm_heap>
        sld:default  "25g" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/num_threads>
        sld:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/reference>
        rdfs:comment        "FastA file for reference genome" ;
        cwl:format          <http://edamontology.org/format_1929> ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "-T"
                            ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".fai" ] ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/bam>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/bam> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/jvm_heap>
        sld:default  "25g" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/num_threads>
        sld:default  1 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/num_threads>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/num_threads> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline>
        a                        cwl:Workflow ;
        rdfs:label               "gridss-germline" ;
        ns1:original_cwlVersion  "v1.1" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/num_threads> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/java_tool_options> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/jvm_heap> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/reference> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline-log> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/cram2bam_log> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/idx> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/vcf> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/java_tool_options>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/java_tool_options> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/java_tool_options>
        sld:default  "" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/idx>
        cwl:outputSource  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/idx> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/log>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).gridss.vcf.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/num_threads>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "-@"
                          ] ;
        sld:default       1 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/cram>
        rdfs:comment      "CRAM to be coverted to BAM" ;
        cwl:format        <http://edamontology.org/format_3462> ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/idx>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).gridss.vcf.idx" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/gridss-germline.cwl#gridss-germline/reference>
        rdfs:comment        "FastA file for reference genome" ;
        cwl:format          <http://edamontology.org/format_1929> ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".pac" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".ann" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".amb" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".sa" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".fai" ] ;
        cwl:secondaryFiles  [ SecondaryFileSchema:pattern
                          ".bwt" ] ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/bam>
        cwl:format         <http://edamontology.org/format_2572> ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cram.nameroot).bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/vcf>
        cwl:format        <http://edamontology.org/format_3016> ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools-cram2bam" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:arguments            ( [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "-b"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "-h"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(inputs.cram.nameroot).bam"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "samtools" "view" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/reference> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/num_threads> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/log> , <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Tools/samtools-cram2bam.cwl#samtools-cram2bam/bam> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ghcr.io/ddbj/jga-analysis/fastq2cram-bqsr-haplotypecaller:1.0.0"
                                 ] ;
        cwl:stderr               "$(inputs.cram.nameroot).bam.log" .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/gridss-germline/jvm_heap>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/jvm_heap> .

<https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/samtools-cram2bam/reference>
        cwl:source  <https://w3id.org/cwl/view/git/22a56d63bd3e05f484032b686d074cc15e3aeed0/per-sample/Workflows/gridss-germline.cwl#gridss-germline/reference> .