@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 cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[2])/$(inputs.tree[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account):$(inputs.PATH[2])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#Apollo_account> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-blat.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-jbrowse.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/protein_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/yml_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/Yml_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#genome_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account):$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account):$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-scaffold-2gmod.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#transcript_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#Yml_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.yml" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-scaffold-2apollo.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#managePy_Path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/yml_file>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/Yml_file> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/managePy_Path>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#managePy_Path> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#cds_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account):$(inputs.PATH[1])/$(inputs.tree[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account):$(inputs.PATH[1])/$(inputs.tree[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#Gmod_account> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-working_files-2gmod.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/managePy_Path>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#managePy_Path> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/create_yml.cwl#Yml_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.yml" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/create_yml.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "genomics-workspace.yml"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "touch" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/create_yml.cwl#Yml_file> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#genome_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#Gmod_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-scaffold-2gmod.dummy" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-scaffold-2gmod.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#host_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account)"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "mkdir -p {$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1]),$(inputs.PATH[1])/$(inputs.tree[0])}"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.Gmod_account)"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "mkdir -p {$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1]),$(inputs.PATH[1])/$(inputs.tree[0])}"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ssh" ) ;
        cwl:baseCommand          ( "ssh" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#Gmod_account> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "createFolder.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#blastdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#cds_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/genome_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#genome_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#create_yml>
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#create_yml/Yml_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/create_yml.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#hmmerdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/protein_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#protein_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/transcript_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#transcript_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "createFolder.dummy" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "createFolder.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#create_yml> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#blastdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#hmmerdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#protein_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#managePy_Path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#Yml_file> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#Yml_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.yml" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '#This yml file is used for genomics-workspace workflow' > genomics-workspace.yml"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl#yml_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl#Yml_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.yml_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#blastdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-blat.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#yml_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#hmmerdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/managePy_Path> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/blastdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/yml_file> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/hmmerdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/PATH> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/Yml_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/protein_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#protein_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/cds_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#cds_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl#Yml_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.yml" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#cds_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_stage_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#protein_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account):$(inputs.PATH[1])/$(inputs.tree[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#PATH> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-working_files-2apollo.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#protein_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-working_files-2gmod.dummy" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-working_files-2gmod.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#login_apollo2_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/cds_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#cds_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/blastdb_Path_production>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#blastdb_Path_production> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/Gmod_account> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#protein_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account):$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#deepPATH_bigwig> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-bigwig.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e 'scientific_name: $(inputs.scientific_name)\ntree: $(inputs.tree)\nmanagePy_Path: $(inputs.managePy_Path)\nblastdb_Path: $(inputs.blastdb_Path_production)\nhmmerdb_Path: $(inputs.hmmerdb_Path_production)\nin_fasta:\n  class: File\n  path: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.genome_fasta_name[0])\nin_fasta_transcript:\n  class: File\n  path: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.transcript_fasta_name[0])\nin_fasta_cds:\n  class: File\n  path: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.cds_fasta_name[0])\nin_fasta_protein: [' >> genomics-workspace.yml"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#blastdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#yml_file> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#hmmerdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#managePy_Path> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#transcript_fasta_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#Yml_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.yml_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#Gmod_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "createFolder.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/hmmerdb_Path_production>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#hmmerdb_Path_production> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account):$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-jbrowse.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/yml_file>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine/Yml_file> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_stage_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/Gmod_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_stage_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml/genome_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#genome_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '${ var A = inputs.protein_fasta_name; var B = '{class: File, path: ' + inputs.PATH[0] + '/' + inputs.tree[0] + '/' + inputs.tree[1] + '/' + inputs.deepPATH_genomic_fasta[0] + '/' + inputs.deepPATH_analyses[0] + '/' + inputs.tree[2] + '/'; var C = []; for (var i = 0; i < A.length; i++) { C = C + B + A[i] + '}'; if(i != A.length-1) { C = C + ','; } } return C; }\n]' >> genomics-workspace.yml"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#yml_file> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#protein_fasta_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#Yml_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.yml_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine/yml_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine/Yml_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#managePy_Path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/Apollo_account>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeFirstLine/yml_file>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#create_yml/Yml_file> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#genome_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodStage> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-blat> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodProd> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#managePy_Path> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#hmmerdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#login_apollo2_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_stage_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#protein_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#blastdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#host_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#genome_fasta_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Yml_file> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/transcript_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#transcript_fasta_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#yml_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-blat.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Yml_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/Yml_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#Yml_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#create_yml/Yml_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-rlvP" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account):$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "rsync" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#PATH> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "dataTransfer-scaffold-2apollo.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/Apollo_account> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2apollo/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/blastdb_Path_production>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#blastdb_Path_production> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#transcript_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/Gmod_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/PATH> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-jbrowse/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-jbrowse.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder-2gmod.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/hmmerdb_Path_production>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#hmmerdb_Path_production> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodProd/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2gmodProd/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.Apollo_account)"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "mkdir -p {$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0]),$(inputs.PATH[1])/$(inputs.tree[0])}"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ssh" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#deepPATH_bigwig> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "createFolder.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#blastdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeFirstLine.cwl#yml_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#Gmod_stage_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/createFolder.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-bigwig.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#hmmerdb_Path_production>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/writeYml-protein-fasta.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#transcript_fasta_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/Apollo_account> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-scaffold-2apollo/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2apollo.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#managePy_Path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#Gmod_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/protein_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/managePy_Path> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/blastdb_Path_production> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/hmmerdb_Path_production> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#create_ymlFile/Yml_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#writeYml-protein-fasta/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2gmod.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#createFolder-2gmodStage/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-working_files-2apollo.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "dataTransfer-working_files-2apollo.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-bigwig.cwl#Apollo_account>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/files_4_Apollo2Server/MoveData/dataTransfer-scaffold-2gmod.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#dataTransfer-working_files-2gmodStage/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/MoveData-workflow.cwl#PATH> .