@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@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 File:  <https://w3id.org/cwl/cwl#File/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/fasta>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#fasta> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#inst_mol>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-inst-mol" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/dbtype>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dbtype" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dbtype" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastfiles>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/blastfiles> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump>
        rdfs:label  "gpx_qdump" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/input_path> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/unzip> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode>
        rdfs:label  "univec_wnode" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/input_jobs> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/blastdb_dir> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/outdir> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnt>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/dbtype>
        sld:default  "nucl" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/ids>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#ids> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#max_batch_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/outdir> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual>
        cwl:in   <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asnt> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/title> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/dbtype> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/softmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/hardmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/fasta> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asnb> ;
        cwl:out  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/blastfiles> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( "-nogenbank" ) ;
                   cwl:arguments     ( "-nogenbank" ) ;
                   cwl:baseCommand   ( "gp_makeblastdb" ) ;
                   cwl:baseCommand   ( "gp_makeblastdb" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/output_db_manifest> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/lds2> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/output_db_file> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/molecules> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_manifest> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/dbtype> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/fasta> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asnb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asnt> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/hardmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_file> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/softmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/title> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/dbname> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/blastfiles> ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  [ Dirent:writable  false ;
                                                      cwl:entry        "$(inputs.molecules)"
                                                    ]
                                     ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  [ Dirent:writable  false ;
                                                      cwl:entry        "$(inputs.molecules)"
                                                    ]
                                     ]
                 ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#affinity>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        sld:default       "subject" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor>
        rdfs:label  "univec_wnode" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/gilist> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/feats> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/hits> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asnt>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnt> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "output.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/dbtype>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#dbtype> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#oseq_ids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.seq_ids_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/hits>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/O>
        rdfs:comment      "Base path to files of output generated from processes" ;
        cwl:inputBinding  [ CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "-O"
                          ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/softmask>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-softmask" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-softmask" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/output_db_file>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-db" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-db" ] ;
        sld:default       "blastdb" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/dbname>
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "$(inputs.output_db_file)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "$(inputs.output_db_file)" ] ;
        sld:type           xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_file>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-found-ids-output" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-found-ids-output" ] ;
        sld:default       "found_ids.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnb>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/title>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-title" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-title" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#queries_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/input>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/input_jobs>
        rdfs:comment      "XML file with input univec jobs, this parameter is _referential_ which CWL does not like.\n" ;
        rdfs:label        "input_jobs" ;
        cwl:inputBinding  [ CommandLineBinding:position  0 ;
                            CommandLineBinding:prefix    "-input-jobs"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir>
        cwl:in   <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastfiles> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastdir> ;
        cwl:out  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastdb> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:arguments     ( [ CommandLineBinding:shellQuote  false ;
                                         cwl:valueFrom                  "mkdir $(inputs.blastdir) && cp"
                                       ]
                                     ) ;
                   cwl:arguments     ( [ CommandLineBinding:shellQuote  false ;
                                         cwl:valueFrom                  "mkdir $(inputs.blastdir) && cp"
                                       ]
                                     ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastdir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastfiles> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastdb> ;
                   cwl:requirements  [ a  cwl:ShellCommandRequirement ] ;
                   cwl:requirements  [ a  cwl:ShellCommandRequirement ]
                 ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asnb>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnb> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/fasta>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening>
        a                        cwl:Workflow ;
        rdfs:label               "foreign_screening" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/contig_ids_out> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/feats> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/out_cache_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/hits> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/hardmask>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#hardmask> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/title>
        sld:default  "BLASTdb created by GPipe" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/hits>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/hits> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#output_xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#asn_cache>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cache_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#subseq_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "gp_makeblastdb" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#softmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#hardmask> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#molecules> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asnt> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#title> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#fasta> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#dbtype> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#lds2> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#blastdb> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/molecules>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/output_db_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-manifest" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-manifest" ] ;
        sld:default       "blastdb.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asnt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asnt" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asnt" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/o>
        sld:default  "fscr_feats.asn" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/softmask>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#softmask> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#hardmask>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#title>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/unzip>
        sld:default  "*" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/feats>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA>
        rdfs:label  "prime_cache" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb>
        sld:default  "blastdb" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#dbtype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#submit_block_template>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-submit-block-template" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#ids_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats>
        rdfs:label  "generate_fscr_feats" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/source> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/o> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/label_suffix> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/input> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/feats> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#subjects_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/asnb>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asnb" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asnb" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/out_cache_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#softmask>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/title>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#title> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#ids>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/hardmask>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hardmask" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hardmask" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode>
        a                        cwl:Workflow ;
        rdfs:comment             "univ_wnode" ;
        rdfs:label               "univec_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/feats> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/hits> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastfiles>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode>
        a                        cwl:CommandLineTool ;
        rdfs:label               "univec_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "univec_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/input_jobs> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/O> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/outdir> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#seq_ids_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-oseq-ids" ] ;
        sld:default       "oseq-ids.seqids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/excluded_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-excluded-seqs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/fasta>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-fasta" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-fasta" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#molinfo>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-molinfo" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.O)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastdir>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/proteins>
        sld:default  [ a              cwl:File ;
                       File:contents  "" ;
                       cwl:basename   "null" ;
                       cwl:path       <file:///dev/null>
                     ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_blastdb_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#batch_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit>
        rdfs:label  "gpx_qsubmit" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/jobs> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#molecules>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.found_ids_output_file)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.found_ids_output_file)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "prime_cache" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "prime_cache" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#seq_ids_name> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#ifmt> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#cache_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#submit_block_template> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#molinfo> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#input> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#inst_mol> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#taxon_db> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#taxid> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#biosource> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#oseq_ids> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/o>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/source>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-source" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/univec_wnode.cwl#univec_wnode/blastdb_dir>
        rdfs:comment  "Hidden parameter, hidden within input_jobs:" ;
        sld:type      cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/run/blastdb>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.blastdir)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.blastdir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:default       "fasta" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#blastdb>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastdb> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#biosource>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-biosource" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/contig_ids_out>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#lds2>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/blastfiles>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blastdb.*" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blastdb.*" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats>
        a                        cwl:CommandLineTool ;
        rdfs:label               "generate_fscr_feats" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "generate_fscr_feats" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/input> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/source> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/excluded_seqs> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/label_suffix> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/o> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/feats> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb>
        rdfs:label  "gp_makeblastdb" ;
        cwl:in      <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/dbtype> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/title> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/fasta> ;
        cwl:out     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> ;
        cwl:run     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#ids>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/generate_fscr_feats.cwl#generate_fscr_feats/label_suffix>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-label-suffix" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#mkdir/blastdir>
        sld:default  "blastdir" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/source>
        sld:default  "vector" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/gilist>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-found-ids-output-manifest" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-found-ids-output-manifest" ] ;
        sld:default       "found_ids.mft" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "This workflow is specialized for the case when there is an LDS2 input  LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n  proteins:\n    default:\n        class: File\n        path: '/dev/null'\n        basename: 'null'\n        contents: ''\n" ;
        rdfs:label               "gpx_qsubmit" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#lds2> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#ids_manifest> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#affinity> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#blastdb> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#subseq_size> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#asn_cache> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#overlap> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#subjects_gc_id_list> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#xml_jobs> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#ids> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#nogenbank> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#NxM_threshold> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#output_xml_jobs> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#proteins> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#queries_gc_id_list> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#batch_size> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/label_suffix>
        sld:default  "Adaptor" .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qsubmit.cwl#NxM_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gp_makeblastdb.cwl#actual/run/ids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/prime_cache.cwl#cache_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-cache" ] ;
        sld:default       "sequence_cache" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gpx_qdump" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-produce-empty-file" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#input_path> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#unzip> , <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/008a090fb1938fbb393494ac8fcb219f0d9f5295/progs/gpx_qdump.cwl#output> .