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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/genome_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#genome_fasta_name> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#tree> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/gff_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/cds_fasta_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gff_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#protein_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scientific_name> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/Current\\ Genome\\ Assembly"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#in_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_bigwig> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/tree> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.protein_fasta_name[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/$(inputs.tree[2])/."
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#protein_fasta_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "analysis_symlink_protein.dummy" .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#gff_name>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

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

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

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

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/deepPATH_genomic_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_genomic_fasta> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scientific_name> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/out_dummy> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#PATH> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-p" ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/1.Genome Assembly/$(inputs.tree[1])/agp"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/1.Genome Assembly/$(inputs.tree[1])/Contigs"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/1.Genome Assembly/$(inputs.tree[1])/Scaffolds"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/$(inputs.tree[2])"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/3.Additional Gene Sets and Annotation Projects"
                                   ]
                                   [ CommandLineBinding:position  6 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/4.Transcriptomes and RNA-Seq"
                                   ]
                                   [ CommandLineBinding:position  7 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/Gaps in Assembly"
                                   ]
                                   [ CommandLineBinding:position  8 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/GC Content"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "mkdir" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl#MAIN_PATH> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "setup_folder.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/gzip_string>
        cwl:outputBinding  [ CommandOutputBinding:glob  "conditional-gzip" ;
                             CommandOutputBinding:outputEval
                                     "$(self[0].contents)" ;
                             cwl:loadContents           true
                           ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob  "conditional-gzip" ;
                             CommandOutputBinding:outputEval
                                     "$(self[0].contents)" ;
                             cwl:loadContents           true
                           ] ;
        sld:type           xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#in_dummy>
        sld:type  cwl:File .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#MAIN_PATH>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/genome_fasta_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-9" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.genome_fasta_name[0])"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#PATH> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "scaffold_gzip.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#MAIN_PATH>
        sld:type  xsd:string .

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

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-9" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gc.bigwig"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gaps.bigwig"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gzip" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#deepPATH_bigwig> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_gzip.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "bigwig_gzip.dummy" .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/deepPATH_bigwig>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#deepPATH_bigwig> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#PATH> .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/protein_fasta_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/out_dummy> .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/scientific_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/tree> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/assembly_symlink.cwl> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink_protein.cwl#MAIN_PATH>
        sld:type  xsd:string .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/gff_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gff_name> .

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

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#MAIN_PATH>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#MAIN_PATH>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bigwig_symlink-gc.dummy" ] ;
        sld:type           cwl:File .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#in_dummy>
        sld:type  cwl:File , sld:null .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#analyses_symlink_protein/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/out_dummy> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#tree> .

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.genome_fasta_name[0]).gz"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/readme.txt"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/1.Genome Assembly/$(inputs.tree[1])/Scaffolds/."
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#deepPATH_genomic_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "scaffold_symlink.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#assembly_symlink/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#MAIN_PATH>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#out_dummy>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bigwig_symlink-gaps.dummy" ] ;
        sld:type           cwl:File .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.transcript_fasta_name[0])"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.cds_fasta_name[0])"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/$(inputs.gff_name[0])"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/$(inputs.deepPATH_analyses[0])/$(inputs.tree[2])/readme.txt"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/2.Official or Primary Gene Set/$(inputs.tree[2])/."
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#cds_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#deepPATH_analyses> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#gff_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#transcript_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#tree> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/analyses_symlink.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "analyses_symlink.dummy" .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/genome_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#genome_fasta_name> .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gc.bigwig.gz"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/GC Content/."
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#in_dummy> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gc.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "bigwig_symlink-gc.dummy" .

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

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip>
        cwl:in    <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/gzip_string> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/tree> ;
        cwl:out   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/out_dummy> ;
        cwl:run   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_gzip.cwl> ;
        cwl:when  "$(inputs.gzip_string == \"\")" .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#in_dummy>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/scientific_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl> .

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/MAIN_PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#MAIN_PATH> .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/gzip_string>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/gzip_string> .

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_gzip/out_dummy> .

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

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

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/scientific_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/PATH> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_symlink/out_dummy> ;
        cwl:run  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/scaffold_symlink.cwl> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/PATH>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#PATH> .

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-s" ;
                                     cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_bigwig[0])/$(inputs.genome_fasta_name[0]).gaps.bigwig.gz"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(inputs.MAIN_PATH)/$(inputs.tree[0])-($(inputs.scientific_name[0])_$(inputs.scientific_name[1]))/$(inputs.tree[1])/5.Other files/Gaps in Assembly/."
                                   ]
                                 ) ;
        cwl:baseCommand          ( "ln" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#MAIN_PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#in_dummy> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#deepPATH_bigwig> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#scientific_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/bigwig_symlink-gaps.cwl#out_dummy> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "bigwig_symlink-gaps.dummy" .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/genome_fasta_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#genome_fasta_name> .

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

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional>
        cwl:in   <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/PATH> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/genome_fasta_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/gzip_string> ;
        cwl:run  [ a                cwl:CommandLineTool ;
                   cwl:arguments    ( [ CommandLineBinding:position  1 ;
                                        cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/"
                                      ]
                                      [ CommandLineBinding:position  2 ;
                                        CommandLineBinding:prefix    "-name" ;
                                        cwl:valueFrom                "$(inputs.genome_fasta_name[0]).gz"
                                      ]
                                    ) ;
                   cwl:arguments    ( [ CommandLineBinding:position  1 ;
                                        cwl:valueFrom                "$(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_genomic_fasta[0])/"
                                      ]
                                      [ CommandLineBinding:position  2 ;
                                        CommandLineBinding:prefix    "-name" ;
                                        cwl:valueFrom                "$(inputs.genome_fasta_name[0]).gz"
                                      ]
                                    ) ;
                   cwl:baseCommand  ( "find" ) ;
                   cwl:baseCommand  ( "find" ) ;
                   cwl:inputs       <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/deepPATH_genomic_fasta> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/genome_fasta_name> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/tree> , <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/PATH> ;
                   cwl:outputs      <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#gzip-conditional/run/gzip_string> ;
                   cwl:stdout       "conditional-gzip"
                 ] .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gaps/scientific_name>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scientific_name> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#bigwig_symlink-gc/tree>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#tree> .

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

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

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#scaffold_gzip/in_dummy>
        cwl:source  <https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/CreateSymlink-workflow.cwl#setup_folder/out_dummy> .

<https://w3id.org/cwl/view/git/b1e1b906fcfb2c0fad8811fb8ab03009282c1d19/flow_reorganize_symlinks/setup_folder.cwl#MAIN_PATH>
        sld:type  xsd:string .

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

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

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

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

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

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