@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 rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_md5checksums>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_trackList_json>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/out_trackList_json> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_1>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_names> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#in_data>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_cds_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_transcript_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_names>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_names> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genomic_fasta>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_genomic_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/in_check>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/out_extract> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#out_names>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/names" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_1> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/url_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/all_url>
        cwl:linkMerge  "merge_flattened" ;
        cwl:pickValue  "all_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/url_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/gap_lines>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "lines-contain-N.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "lines-contain-N.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_tracks>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl#out_gaps_bigwig>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_fasta.basename).gaps.bigwig" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo '$(inputs.url[0])' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#url> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#readme_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_cds_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/url> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gc_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/in_gz>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#processed_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_cds_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_cds_fasta> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_GO>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "--gaf"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/in_fai> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/in_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_tracks_conf> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/in_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/in_trackList_json> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/out_trackList_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "$(inputs.in_data.location.slice(7))"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#deepPATH> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_PathAnnotatorGMT>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "--verbose"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "--out" ;
                                     cwl:valueFrom                "data/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "generate-names.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#in_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#in_data> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#out_names> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_data)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not/fasta_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not/gap_lines> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_transcript_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "faidx"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "samtools" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl#out_fai> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/in_txt>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#create_readme>
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#create_readme/readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/create_readme.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not/fasta_file>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/in_gz>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_protein_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/url> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_protein_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_extract>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_check>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-c" ;
                                     cwl:valueFrom                "$(inputs.in_check.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "md5sum" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#in_check> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#out_check> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = inputs.in_gz; LIST.push(inputs.in_check); return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "${ var X = (inputs.in_check); return X.nameroot + '.log'; }" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#blastdb_Path_stage>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#processed_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_protein_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/out_gz> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_PathAnnotatorGMT>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_PathAnnotatorGMT> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_seq> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/gff_release_number>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gff_release_number> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/in_fasta> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/out_gaps_bigwig> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl> ;
        cwl:when  "$(inputs.gap_lines.size > 0)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-df" ;
                                     cwl:valueFrom                "$(inputs.in_gz.basename)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-df" ;
                                     cwl:valueFrom                "$(inputs.in_gz.basename)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-df" ;
                                     cwl:valueFrom                "$(inputs.in_gz.basename)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-df" ;
                                     cwl:valueFrom                "$(inputs.in_gz.basename)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-df" ;
                                     cwl:valueFrom                "$(inputs.in_gz.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#in_gz> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#out_gz> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_gz)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_gz)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_gz)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_gz)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_gz)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename).gaps.bigwig"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gap2bigwig.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl#out_gaps_bigwig> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry  "$(inputs.in_fasta)" ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/original_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_md5checksums>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#url_string>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_tracks>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_tracks> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#in_2bi>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#out_trackList_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trackList.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#out_trackList_json_bak>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trackList.json.bak-metadata" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/deepPATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/organization>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#organization> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#managePy_Path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-si" ;
                                     cwl:valueFrom                "../../scaffold/bigwig"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-t" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#out_tracks>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/tracks/" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/fasta_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/id_deleted_file> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-v" ;
                                         cwl:valueFrom                ">"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.fasta_file.basename)"
                                       ]
                                     ) ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-v" ;
                                         cwl:valueFrom                ">"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.fasta_file.basename)"
                                       ]
                                     ) ;
                   cwl:baseCommand   ( "grep" ) ;
                   cwl:baseCommand   ( "grep" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/fasta_file> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/id_deleted_file> ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.fasta_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.fasta_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:stdout        "id_deleted_file.txt"
                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/in_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/url_string> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl> ;
        cwl:when  "$(inputs.url_string != \"NA NA NA NA NA\\n\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/in_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/in_trackList_json> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/out_trackList_json> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl> ;
        cwl:when  "$(inputs.gap_lines.size > 0)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_extract>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#gff_release_number>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_2bi>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genomic_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_apollo2_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/in_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/in_trackList_json> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/out_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/out_trackList_json> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_trackList_json>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_extract> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#tree> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_genePrediction_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_assembly_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_names> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap_lines>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_names>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_names> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_1> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/link_to_publication>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#link_to_publication> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig/in_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig/out_gc_bigwig> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#in_gz>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/url> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_protein_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_extract> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl> ;
        cwl:when  "$(inputs.url_string != \"NA NA NA NA NA\\n\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_trackList_json>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/organization>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#organization> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/in_txt> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/url_string> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/out_extract> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl> ;
        cwl:when  "$(inputs.url_string != \"NA NA NA NA NA\\n\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_protein_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#in_gz>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/url_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nInformation about this dataset can be found here: \nInformation about the publications of this dataset can be found here: $(inputs.link_to_publication)' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#link_to_publication> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#out_trackList_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/trackList.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_transcript_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_genomic_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_extract>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/out_extract> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_genePrediction_readme>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genePrediction_readme> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/fasta_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gff_release_number> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_2bi> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_gc_bigwig> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/in_gz>
        cwl:linkMerge  "merge_flattened" ;
        cwl:pickValue  "all_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_seq>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_seq> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/gff_release_number>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gff_release_number> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/in_gz>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#processed_gff>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.annotated.gff3" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/id_deleted_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme>
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/create_readme.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#url_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#in_data>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/in_gz> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/out_gz> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl> ;
        cwl:when  "$(inputs.url_protein_fasta != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/processed_gff> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> ;
        cwl:when  "$(inputs.processed_gff != null)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#processed_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl#out_gc_bigwig>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_fasta.basename).gc.bigwig" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_transcript_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_trackList_json_bak>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json_bak> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/url_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_md5checksums>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json_bak>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/run/id_deleted_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "id_deleted_file.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "id_deleted_file.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_gaps_bigwig>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/out_gaps_bigwig> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_cds_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_extract> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_check> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/in_trackList_json>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/out_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#in_2bi> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/original_gff>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeLastLine>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeLastLine/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeLastLine/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#in_gc_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/in_gff>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "${ var A = inputs.in_gz; var B = []; for (var i = 0; i < A.length; i++) { B = B + A[i].basename; if(i != A.length-1) { B = B + '|'; } } return B; }"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.in_txt.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "egrep" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#in_txt> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#in_gz> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#out_extract> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_txt)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "md5checksums.txt2" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#create_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeLastLine> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#scientific_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-path" ;
                                     cwl:valueFrom                "flatfile-to-json.pl"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     CommandLineBinding:prefix    "-gff" ;
                                     cwl:valueFrom                "$(inputs.in_gff.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-out" ;
                                     cwl:valueFrom                "data/"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     CommandLineBinding:prefix    "-organism" ;
                                     cwl:valueFrom                "$(inputs.scientific_name[0])_$(inputs.scientific_name[1])"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "-trackLabel1" ;
                                     cwl:valueFrom                "$(inputs.tree[0])_current_models"
                                   ]
                                   [ CommandLineBinding:position  6 ;
                                     CommandLineBinding:prefix    "-release" ;
                                     cwl:valueFrom                "$(inputs.gff_release_number)"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "-source" ;
                                     cwl:valueFrom                "$(inputs.url_genomic_gff[0])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "add_NCBI_annotation_track.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#gff_release_number> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#in_data> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#out_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#out_tracks> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_gff), (inputs.in_data)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#in_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_protein_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_md5checksums>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_protein_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#out_check>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "${ var X = (inputs.in_check); return X.nameroot + '.log'; }" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#gap_lines>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/url> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_check>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_gc_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gc_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta/in_url> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.in_url != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_assembly_readme>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_assembly_readme> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#in_gz>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_check>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#path_GO>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_egap>
        sld:default  false ;
        sld:type     xsd:boolean .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#create_readme/readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_assembly_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_2bi> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_extract> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genePrediction_readme> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit/in_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit/out_2bi> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_gc_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_gc_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#in_data> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/readme_file> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2/out_readme_file> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl> ;
        cwl:when  "$(inputs.path_GO != null)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_trackList_json_bak>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_trackList_json_bak> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_seq>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl#in_url>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/create_readme.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "touch" ) ;
        cwl:baseCommand          ( "touch" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/create_readme.cwl#readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gaps_bigwig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/path_GO> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-si" ;
                                     cwl:valueFrom                "../../scaffold/analyses"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-t" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not/gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#in_gaps_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "--fasta" ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "--out" ;
                                     cwl:valueFrom                "data/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "prepare-refseqs.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:hints                [ a                ns1:LoadListingRequirement ;
                                   cwl:loadListing  "shallow_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#in_fai> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_data> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_fasta), (inputs.in_fai) ]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#in_txt>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_names>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nInformation about this dataset can be found here: \nInformation about the publication of this dataset can be found here: $(inputs.link_to_publication)' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#link_to_publication> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#out_readme_file> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_2bi>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_2bi> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/url_genomic_gff> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/out_gz> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl> ;
        cwl:when  "$(inputs.url_genomic_gff != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/original_gff>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nThe file $(inputs.original_gff.basename) was post-processed to add functional annotations from the AgBase functional annotation pipeline (https://github.com/agbase). The resulting file is: $(inputs.processed_gff.basename). This file was used for all operations within the i5k Workspace.' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#original_gff> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred_annotation.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeLastLine/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nThe file [file] was post-processed to [describe post-processing, if any]. The resulting file is: [Filename]. This file was used for all operations within the i5k Workspace.' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl#readme_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_transcript_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/in_dummy> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/out_gz> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl> ;
        cwl:when  "$(inputs.url_genomic_fasta != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_transcript_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_cds_fasta>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/deepPATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_2>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/organization>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#organization> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_protein_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  6 ;
                                     CommandLineBinding:prefix    "--out" ;
                                     cwl:valueFrom                "$(inputs.in_gff.nameroot + \".annotated.gff3\")"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "add_ontology_terms_from_gaf_gmt.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#annotate_egap> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#annotate_cds> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_PathAnnotatorGMT> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_GO> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_trackList_json_bak>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/out_trackList_json_bak> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_gaps_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_gaps_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_cds_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_analyses/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_seq>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_seq> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl#out_wget>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_1[0])/$(inputs.deepPATH_2[0])/$(inputs.tree[2])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#tree> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_md5checksums>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_string>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/url_string> ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gff_release_number>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#in_tracks>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#out_dummy>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_assembly_readme>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/in_tracks>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_tracks> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_extract> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_2bi> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genePrediction_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_tracks> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_assembly_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_tracks_conf> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#link_bigwig/in_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_seq>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/url> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gap_lines>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/gap_lines> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/all_url> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/url_string> ;
        cwl:run  [ a                cwl:CommandLineTool ;
                   cwl:arguments    ( [ CommandLineBinding:position  1 ;
                                        cwl:valueFrom                "$(inputs.all_url)"
                                      ]
                                    ) ;
                   cwl:arguments    ( [ CommandLineBinding:position  1 ;
                                        cwl:valueFrom                "$(inputs.all_url)"
                                      ]
                                    ) ;
                   cwl:baseCommand  ( "echo" ) ;
                   cwl:baseCommand  ( "echo" ) ;
                   cwl:inputs       <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/run/all_url> ;
                   cwl:outputs      <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/run/url_string> ;
                   cwl:stdout       "output.txt"
                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_trackList_json.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.in_trackList_json.basename).bak-metadata"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename).gc.bigwig"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename).gaps.bigwig"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "add_metadata_to_GC_gap_bigwig_tracks.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#out_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#out_trackList_json> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_fasta), (inputs.in_trackList_json)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/url_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#readme_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme/readme_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/PATH> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/in_dummy> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/out_gz> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl> ;
        cwl:when  "$(inputs.url_transcript_fasta != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_seq>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/seq/" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_gaps_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_gaps_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/id_deleted_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/id_deleted_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/deepPATH_2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/extract_md5checksums.cwl#out_extract>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "md5checksums.txt2" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_gff>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/link_to_publication>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#link_to_publication> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_string>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_protein_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v2> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeFirstLine> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#create_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#path_GO> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#original_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_extract/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_extract> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genomic_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genomic_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_protein_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_transcript_fasta> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl#in_data>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/in_fai>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx/out_fai> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#in_data> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_genomic_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_apollo2_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#url>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        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/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_GO>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_GO> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/url_genomic_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/readme_file> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeLastLine_v1/out_readme_file> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl> ;
        cwl:when  "$(inputs.path_GO == null)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_apollo2_data>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#hmmerdb_Path_stage>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genePrediction_readme>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "setup_folder.dummy" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/in_gc_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig/out_gc_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_trackList_json_bak> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_tracks>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_tracks> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_gc_bigwig>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig/out_gc_bigwig> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/run/all_url>
        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/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta/in_url> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_fasta/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.in_url != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo 'The following files were retrieved from $(inputs.organization) on ${var A = new Date(); var year = A.getFullYear(); var month = A.getMonth()+1; var day = A.getDate(); var date = year + '-' + day + '-' + month;  return date;}:' > readme.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo 'The following files were retrieved from $(inputs.organization) on ${var A = new Date(); var year = A.getFullYear(); var month = A.getMonth()+1; var day = A.getDate(); var date = year + '-' + day + '-' + month;  return date;}:' > readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#organization> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_cds_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_assembly_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/id_deleted_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/gap_lines> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-ne" ;
                                         cwl:valueFrom                "print if /N/"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.id_deleted_file.basename)"
                                       ]
                                     ) ;
                   cwl:arguments     ( [ CommandLineBinding:position  1 ;
                                         CommandLineBinding:prefix    "-ne" ;
                                         cwl:valueFrom                "print if /N/"
                                       ]
                                       [ CommandLineBinding:position  2 ;
                                         cwl:valueFrom                "$(inputs.id_deleted_file.basename)"
                                       ]
                                     ) ;
                   cwl:baseCommand   ( "perl" ) ;
                   cwl:baseCommand   ( "perl" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/id_deleted_file> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not/run/gap_lines> ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.id_deleted_file)]; return LIST; }"
                                     ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a  cwl:InlineJavascriptRequirement ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  "${ var LIST = [(inputs.id_deleted_file)]; return LIST; }"
                                     ] ;
                   cwl:stdout        "lines-contain-N.txt"
                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_trackList_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/trackList.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#out_trackList_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trackList.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/in_trackList_json>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#in_trackList_json>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_transcript_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/organization>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#organization> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_check>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_seq>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_seq> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename).2bi"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "faToTwoBit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl#out_2bi> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_fasta)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_protein_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_assembly_readme> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_transcript_fasta>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_2bi>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#faToTwoBit/out_2bi> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/path_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_md5checksums/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_1>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_genomic_gff>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_gff/out_gz> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_tracks_conf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#prepare-refseqs/out_tracks_conf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_cds_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_cds_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_cds_fasta/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_original_genomic_gff/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_md5checksums>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_GO>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx/in_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx/out_fai> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_transcript_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#extract_md5checksums/in_gz>
        cwl:linkMerge  "merge_flattened" ;
        cwl:pickValue  "all_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/link_to_publication>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#link_to_publication> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/link_to_publication>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#link_to_publication> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_cds_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id/fasta_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_data>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_extract>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_extract> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_names>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/url_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_bigwig>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#in_fai>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not/gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/in_2bi>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_2bi> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta/in_url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_cds_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeInfo/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#samtools_faidx/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/annotate_cds> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/annotate_egap> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_GO> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/in_PathAnnotatorGMT> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/processed_gff> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/in_fasta>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/in_gaps_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/out_gaps_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_protein_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2blat/in_2bi> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#gap_lines>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-gff/url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap2bigwig/gap_lines>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gap_lines> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/scientific_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme/readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#cp_check/in_data> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/cp_file.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.in_data.basename)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[2])/$(inputs.tree[0])/"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "cp" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#PATH> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.in_data)"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#deepPATH_2>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_cds_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/out_gz> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/deepPATH_analyses>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_analyses> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_protein_fasta/in_gz>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/deepPATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/tree> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl> ;
        cwl:when  "$(inputs.gap_lines.size > 0)" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#gff_release_number>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/in_url> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/url_string> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.url_string != \"NA NA NA NA NA\\n\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-protein/url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#annotate_egap>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--egap"
                          ] ;
        sld:default       false ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_bigwig.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gc/in_trackList_json>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add-bw-track_gaps/out_trackList_json> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/in_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/in_tracks> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/out_names> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/generate-names.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#add_metadata/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#GCcontent2bigwig/in_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#in_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/gff_release_number> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/gap_lines> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/in_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/url_genomic_gff> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_gc_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_trackList_json_bak> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_gaps_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_seq> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_tracks_conf> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_names> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_2bi> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_tracks> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_protein_fasta>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_protein_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/gap2bigwig.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_genomic_gff>
        cwl:pickValue  "first_non_null" ;
        cwl:source     <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/processed_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#url_transcript_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_1> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/deepPATH_2> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo-genePred.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks_conf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genePrediction_readme> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#cp_2bi/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/workflow.cwl#in_2bi> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_genePrediction_readme>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#annotate_cds>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--cds"
                          ] ;
        sld:default       false ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/samtools_faidx.cwl#out_fai>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.fai" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_gff>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--gff"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#OUT_names>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#generate-names/out_names> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#readme_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#create_readme/readme_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_transcript_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_genomic_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/create_readme.cwl#readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_assembly_readme/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_check>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl#out_gz>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_gz.nameroot)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_gz.nameroot)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_gz.nameroot)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_gz.nameroot)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_gz.nameroot)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_cds_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#organization>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "--pos_color" ;
                                     cwl:valueFrom                "rgba(0,0,255,50)"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "--neg_color" ;
                                     cwl:valueFrom                "rgba(255,255,0,50)"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "--bicolor_pivot" ;
                                     cwl:valueFrom                "0.5"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "--label" ;
                                     cwl:valueFrom                "GC Content"
                                   ]
                                   [ CommandLineBinding:position  9 ;
                                     CommandLineBinding:prefix    "--bw_url" ;
                                     cwl:valueFrom                "bigwig/$(inputs.in_gc_bigwig.basename)"
                                   ]
                                   [ CommandLineBinding:position  11 ;
                                     CommandLineBinding:prefix    "--in" ;
                                     cwl:valueFrom                "$(inputs.in_trackList_json.basename)"
                                   ]
                                   [ CommandLineBinding:position  13 ;
                                     CommandLineBinding:prefix    "--out" ;
                                     cwl:valueFrom                "trackList.json"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "add-bw-track.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#in_gc_bigwig> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gc.cwl#out_trackList_json> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_gc_bigwig), (inputs.in_trackList_json)]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gaps-or-not> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#delete_id> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#fasta_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/gaps_or_not.cwl#gap_lines> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_string> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/path_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/url_cds_fasta> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_check> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_extract> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/OUT_cds_fasta> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "echo -e '\nThe file was post-processed to [describe post-processing, if any]. The resulting file is: [Filename]. This file was used for the JBrowse genome browser and the Apollo manual curation tool.' >> readme.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bash" "-c" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl#readme_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeLastLine-genePred.cwl#out_readme_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.readme_file)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/faToTwoBit.cwl#out_2bi>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.2bi" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_annotated_genomic_gff/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_seq/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_transcript_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_transcript_fasta/out_gz> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file_4_annotation.cwl#in_data>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_protein_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#OUT_genomic_fasta>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/out_gz> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/readme_file>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-cds/out_readme_file> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_genomic_gff>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gc_bigwig>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "--pos_color" ;
                                     cwl:valueFrom                "black"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "--neg_color" ;
                                     cwl:valueFrom                "white"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "--label" ;
                                     cwl:valueFrom                "Gaps in assembly"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "--bw_url" ;
                                     cwl:valueFrom                "bigwig/$(inputs.in_gaps_bigwig.basename)"
                                   ]
                                   [ CommandLineBinding:position  9 ;
                                     CommandLineBinding:prefix    "--in" ;
                                     cwl:valueFrom                "$(inputs.in_trackList_json.basename)"
                                   ]
                                   [ CommandLineBinding:position  11 ;
                                     CommandLineBinding:prefix    "--out" ;
                                     cwl:valueFrom                "trackList.json"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "add-bw-track.pl" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#in_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#in_gaps_bigwig> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#out_trackList_json> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_gaps_bigwig), (inputs.in_trackList_json)]; return LIST; }"
                                 ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_assembly_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gaps_or_not> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#managePy_Path> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_apollo2_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_egap> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#hmmerdb_Path_stage> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#gff_release_number> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_PathAnnotatorGMT> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_protein_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_cds> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_transcript_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_md5checksums> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#blastdb_Path_stage> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_GO> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_cds_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_analyses> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#path_protein_fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gc_bigwig/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_tracks_conf>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#apollo2_data_processing/OUT_tracks_conf> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/in_gz> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/in_dummy> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/url_cds_fasta> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/out_gz> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/gunzip_single.cwl> ;
        cwl:when  "$(inputs.url_cds_fasta != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/annotate_egap>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_egap> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:baseCommand          ( "wget" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl#in_url> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl#out_wget> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#link_to_publication>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/run/url_string>
        cwl:outputBinding  [ CommandOutputBinding:glob  "output.txt" ;
                             CommandOutputBinding:outputEval
                                     "$(self[0].contents)" ;
                             cwl:loadContents           true
                           ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob  "output.txt" ;
                             CommandOutputBinding:outputEval
                                     "$(self[0].contents)" ;
                             cwl:loadContents           true
                           ] ;
        sld:type           xsd:string .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/in_gff> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/tree> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/gff_release_number> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/in_data> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/url_genomic_gff> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_trackList_json> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#flatfile-to-json/out_tracks> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeURL.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_tracks_conf/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_tracks_conf> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#setup_folder/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "creating directory tree" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-p" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/jbrowse/data"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/bigwig"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.PATH[1])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/remap"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(inputs.PATH[2])/$(inputs.tree[0])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "mkdir" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#PATH> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/setup_folder.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "setup_folder.dummy" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#readme_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#dispatch/in_md5checksums>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_md5checksums> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/check_md5checksums.cwl#in_check>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_transcript_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/tree>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/original_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#original_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/url_cds_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_cds_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_genomic_fasta/in_gz>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#in_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_gaps_bigwig/in_data>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_gaps_bigwig> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#deepPATH_analyses>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename).gc.bigwig"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.in_fasta.basename)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "GCcontent2bigwig.py" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl#in_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/GCcontent2bigwig.cwl#out_gc_bigwig> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "${ var LIST = [(inputs.in_fasta) ]; return LIST; }"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/link_analyses.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff/in_url> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_genomic_gff/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.in_url != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/in_extract>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_extract> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/processed_gff>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#processed_gff> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta/in_url> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_protein_fasta/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.in_url != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add-bw-track_gaps.cwl#out_trackList_json>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "trackList.json" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#writeURL-transcript/url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-genePrediction-workflow.cwl#url_transcript_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#md5checksums/in_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#download/OUT_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_transcript_fasta/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#OUT_md5checksums>
        cwl:outputSource  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/out_wget> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/workflow.cwl#url_genomic_gff>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#path_genomic_gff>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/add-annotation/add_annotation.cwl#in_PathAnnotatorGMT>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--gmt"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#gunzip_cds_fasta/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_md5checksums/workflow.cwl#check_md5checksums/out_check> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_names/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_cds>
        sld:default  false ;
        sld:type     xsd:boolean .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#url_md5checksums>
        sld:type  sld:null ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_genePrediction_readme/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#PATH> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#deepPATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_cds_fasta>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#url_md5checksums>
        sld:type  sld:null ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_file.cwl#tree>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/add_metadata.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#add_annotation/annotate_cds>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#annotate_cds> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/flatfile-to-json.cwl#scientific_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2blat/cp_file.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#out_tracks_conf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "data/tracks.conf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#cp_trackList_json_bak/deepPATH>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#deepPATH_apollo2_data> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2working_files/workflow.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#PATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/link_to_publication> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/readme_file> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/scientific_name> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeInfo/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeInfo.cwl> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/cp_dir.cwl#deepPATH>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#original_gff>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/2other_species/workflow.cwl#in_genomic_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2other_species/in_tracks_conf>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#in_tracks_conf> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#create_genePrediction_readme/path_GO>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/final-workflow.cwl#path_GO> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl#out_readme_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "readme.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeURL/url>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#url_genomic_fasta> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_apollo2_data_processing/processing/prepare-refseqs.cwl#in_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta>
        cwl:in    <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta/in_url> ;
        cwl:out   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_transcript_fasta/out_wget> ;
        cwl:run   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/wget_single.cwl> ;
        cwl:when  "$(inputs.in_url != \"NA\" )" .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#2working_files/url_string>
        cwl:source  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_dispatch/workflow.cwl#url_string> .

<https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine>
        cwl:in   <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/organization> , <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/readme_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/readme-assembly-workflow.cwl#writeFirstLine/out_readme_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_create_readme/writeFirstLine.cwl> .