@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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/contam_in_prok_blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contam_in_prok_blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results>
        rdfs:label  "align_filter" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/filter> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/subject_allowlist> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/o> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/onon_match> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/best_hit_overhang>
        sld:default  1e-01 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#evalue>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-evalue" ] ;
        sld:default       1e-02 ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/perc_identity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/evalue> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/best_hit_overhang> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/max_target_seqs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/dust> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/soft_masking> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/word_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/task> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/best_hit_score_edge> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/input_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/swap_rows> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#inst_mol> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#seq_ids_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#taxon_db> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#cache_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#molinfo> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#submit_block_template> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#biosource> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#taxid> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#oseq_ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/evalue>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#evalue> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#perc_identity>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-perc_identity" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/outdir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#ids_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids-manifest" ] ;
        sld:default       "ids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_target_seqs>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output_glob>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/calls>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/calls> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#it>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-it" ] ;
        sld:default       false ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#queries_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-queries-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_glob)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_overhang>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#perc_identity>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/title>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#title> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output_glob>
        sld:default  "blast.*.asn" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#softmask>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/ignore_all_errors>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/ifmt>
        sld:default  "seq-align-set" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#best_hit_overhang>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-best_hit_overhang" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/input>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blast_align> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "" ;
        rdfs:label               "align_find_frequent_sas" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_find_frequent" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/align> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/out_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/row> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/threshold> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/frequent> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align_filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#filter> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#o_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#nogenbank> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#subject_allowlist> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#onon_match_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#input_mft> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#o> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#onon_match> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# aligns.mft created for align_filter from input \"input\" Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "aligns.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/label_suffix>
        sld:default  "contam_in_prok" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#max_reblast_spans>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-reblast-spans" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#calls_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "calls.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#subseq_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subseq-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/swap_rows>
        sld:default  false .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "generate_fscr_feats" ) ;
        cwl:baseCommand          ( "generate_fscr_feats" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/excluded_seqs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/label_suffix> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/source> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/o> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/feats> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#soft_masking>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-soft_masking" ] ;
        sld:default       true ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asnb>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnb> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls/calls> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls/o> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/soft_masking>
        sld:default  "true" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/task>
        sld:default  "blastn" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/source>
        sld:default  "vector" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#success>
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "$(true)" ] ;
        sld:type           xsd:boolean .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/out_cache_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#proteins>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb>
        sld:default  "blastdb" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/hardmask>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#hardmask> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#max_target_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_target_seqs" ] ;
        sld:default       250 ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor>
        rdfs:label  "univec_wnode" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/gilist> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/hits> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#output_xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/gilist>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#asn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "gp_makeblastdb" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#dbtype> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#hardmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#lds2> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#softmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#molecules> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#title> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#blastdb> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_blastdb_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#affinity>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-affinity" ] ;
        sld:default       "subject" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#ids>
        sld:type  sld:null ;
        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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/input>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/o> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contig_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/perc_identity>
        sld:default  90 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/out_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out" ] ;
        sld:default       "frequent.seq_ids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "tt_fscr_calls_pass1" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#calls> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#biosource>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-biosource" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#blastdb>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/blastdb> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/perc_identity>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#perc_identity> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "tt_blastn_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#word_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#perc_identity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#evalue> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#affinity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#dust> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#soft_masking> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#ids_out> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_overhang> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_score_edge> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#task> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_target_seqs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blast_align> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/o>
        sld:default  "feats.asn" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:default       "*" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/blast_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#ignore_all_errors>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ignore-all-errors" ] ;
        sld:default       false ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#input_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "aligns.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/evalue>
        sld:default  1e-04 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#subjects_gc_id_list>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subjects-gc-id-list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "blastn_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "blastn_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#task> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#dust> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#swap_rows> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#word_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#soft_masking> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#perc_identity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#max_target_seqs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#evalue> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#best_hit_overhang> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#best_hit_score_edge> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#outdir> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits>
        rdfs:label  "align_find_frequent_sas" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits/align> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits/frequent> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.O)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#asn_cache>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cache_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/source>
        sld:default  "vector" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          sld:null ;
        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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blast_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/adaptor_blastdb_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_blastdb_dir> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#molecules>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/blastdir>
        sld:default  "blastdir" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contig_gilist>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output>
        sld:default  "blast.#.asn" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/dbtype>
        sld:default  "nucl" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/dust>
        sld:default  "yes" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#molinfo>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-molinfo" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_batch_length>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#o>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.oname)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/fasta>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#xml_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#overlap> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#ids_manifest> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#NxM_threshold> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#queries_gc_id_list> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#max_batch_length> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#proteins> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#batch_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#lds2> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#nogenbank> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#output_xml_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#subseq_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#affinity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#subjects_gc_id_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#jobs> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   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        "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ 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        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path  + '\\n';}return blob;}" ;
                                                  cwl:entryname  "ids.mft"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#masked_locs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.masked_locs_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#dbtype>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/best_hit_score_edge>
        sld:default  1e-01 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/max_batch_length>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_batch_length> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/o>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening>
        a                        cwl:Workflow ;
        rdfs:label               "bacterial_screening" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contam_in_prok_blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contig_gilist> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/filtered_align> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/blast_align> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_score_edge>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/filtered_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/o> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asnt>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnt> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane>
        rdfs:comment  "corresponds to part of default plane in foreign contamination screening graph of classic Gpipe it does bunch of generic things so it has to be first" ;
        rdfs:label    "foreign_screening" ;
        cwl:in        <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_fasta> ;
        cwl:out       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_ids_out> ;
        cwl:run       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/softmask>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#softmask> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/foreign_feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit>
        rdfs:label  "gpx_qsubmit" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/ids> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/jobs> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#inst_mol>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-inst-mol" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#subject_allowlist>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subject-allowlist" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#onon_match_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-non-match-output" ] ;
        sld:default       "align-nomatch.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#calls>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls/o> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#num_partitions>
        rdfs:comment      "this parameter is fixed for this command line workflow, because the output is defined as single file\n" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-num-partitions" ] ;
        sld:default       1 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#batch_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-batch-size" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/tab>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/calls> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#ids_out>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/ignore_all_errors>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/ignore_all_errors> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/input_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/O> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/outdir> ;
        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)"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening>
        rdfs:comment  "corresponds to bacterial_screening plane in in foreign contamination screening graph of classic Gpipe" ;
        rdfs:label    "bacterial_screening" ;
        cwl:in        <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/contig_gilist> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/contam_in_prok_blastdb_dir> ;
        cwl:out       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/filtered_align> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/blast_align> ;
        cwl:run       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/hits> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/feats> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/ignore_all_errors> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/tab> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/success> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1>
        rdfs:label  "fscr_calls_pass1" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/max_reblast_spans> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/repeat_threshold> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/calls> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/masked_locs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/reblast_locs> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#o_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contam_in_prok_blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/outdir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#calls>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.calls_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/contig_gilist>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_ids_out> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/filtered_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/filtered_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#title>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/fasta>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#fasta> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/task>
        sld:default  "megablast" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/ids_out>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contig_gilist> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb>
        rdfs:label  "gp_makeblastdb" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/title> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/dbtype> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/fasta> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/hardmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asnb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/dbtype> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/softmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/title> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/asnt> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/asnt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/molecules> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/title> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/softmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/output_db_file> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/dbtype> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_file> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/lds2> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/asnb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/hardmask> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/output_db_manifest> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/found_ids_output_manifest> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/asn_cache> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/found_ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/blastfiles> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/dbname> ;
                   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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#input_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "input.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#word_size>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contamination_feats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/feats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#dust>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/align>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl#univec_wnode/asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/word_size>
        sld:default  28 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA>
        rdfs:label  "prime_cache" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/frequent>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#onon_match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.onon_match_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blastdb>
        sld:default  "contam_in_prok" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#soft_masking>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnb>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#input_path> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#output_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#unzip> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl#output> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#ids>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdb" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/label_suffix>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-label-suffix" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-label-suffix" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/o> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/source> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/label_suffix> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/feats> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/contig_ids_out> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/out_cache_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/hits> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#dust>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-dust" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/num_partitions>
        sld:default  1 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#word_size>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-word_size" ] ;
        sld:default       12 ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits/align>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blast_align> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/feats>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/proteins>
        sld:default  [ a              cwl:File ;
                       File:contents  "" ;
                       cwl:basename   "null" ;
                       cwl:path       <file:///dev/null>
                     ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/word_size> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/best_hit_overhang> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/perc_identity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/dust> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/best_hit_score_edge> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/task> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/ids_out> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/evalue> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blastdb> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/contig_ids_out>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "fscr_format_calls" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" "-no-taxon-access" ) ;
        cwl:baseCommand          ( "fscr_format_calls" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#oname> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#calls> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#o> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/excluded_seqs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-excluded-seqs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-excluded-seqs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/blastfiles>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/blastfiles> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contig_fasta> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/hits>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump>
        rdfs:label  "gpx_qdump" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/input_path> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/unzip> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/repeat_threshold>
        sld:default  300 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#oname>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "calls.tab" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/affinity>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#affinity> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_xml_jobs)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#o>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen>
        a                        cwl:Workflow ;
        rdfs:label               "vecscreen" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contam_in_prok_blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/ignore_all_errors> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contig_fasta> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/adaptor_fasta> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/foreign_feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/blast_align> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/calls> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/hits> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/filtered_align> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/adaptor_blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/success> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/out_cache_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contamination_feats> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/contig_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asn_cache>
        sld:type  [ sld:items  cwl:Directory ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/ifmt>
        sld:default  "seq-annot" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/success>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/screen_evaluate/success> ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/ids>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#ids> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gpx_make_outputs" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "gpx_make_outputs" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#num_partitions> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#input_path> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output_glob> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#unzip> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl#output_file> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-threshold" ] ;
        sld:default       10 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#fasta>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gilist> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#overlap>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-overlap" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/BLAST_Against_contam_in_prok/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:default       "seq-align-set" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_format_calls.cwl#calls>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-calls" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#reblast_locs_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-reblast-locs" ] ;
        sld:default       "reblast_locs.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#task>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/prime_cache.cwl#oseq_ids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.seq_ids_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#affinity>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/adaptor_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/dbtype>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#dbtype> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#masked_locs_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-masked-locs" ] ;
        sld:default       "masked_locs.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/best_hit_overhang>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_overhang> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#lds2>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#reblast_locs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.reblast_locs_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#best_hit_score_edge>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-best_hit_score_edge" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "fscr_calls_pass1" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "fscr_calls_pass1" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#max_reblast_spans> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#repeat_threshold> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#masked_locs_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#calls_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#reblast_locs_name> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#input_manifest> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#masked_locs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#calls> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#reblast_locs> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# input.mft created for fscr_calls_pass1 from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "input.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/input>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/output> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#hardmask>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#swap_rows>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-swap-rows" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/blastn_wnode.cwl#task>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-task" ] ;
        sld:default       "blastn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/contam_in_prok_blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/input>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#input> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#NxM_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-NxM-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#filter>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-filter" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/blastfiles> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/blastdir> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/run/blastfiles> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/run/blastdir> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#mkdir/run/blastdb> ;
                   cwl:requirements  [ a  cwl:ShellCommandRequirement ] ;
                   cwl:requirements  [ a  cwl:ShellCommandRequirement ]
                 ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#evalue>
        sld:type  xsd:float .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb_dir> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/ids> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/affinity> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/max_batch_length> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/blastdb> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/nogenbank> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/proteins> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl#generate_fscr_feats/source>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-source" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-source" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/ids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#ids_out> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "screen_evaluate" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "screen_evaluate" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#tab> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#asn> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#ignore_all_errors> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#ifmt> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#it> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#success> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode>
        rdfs:label  "univec_wnode" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/input_jobs> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/asn_cache> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/univec_wnode/outdir> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/univec_wnode.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/max_reblast_spans>
        sld:default  50000 .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#actual/run/molecules>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features>
        rdfs:label  "generate_fscr_feats" ;
        cwl:in      <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/o> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/source> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/label_suffix> ;
        cwl:out     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Generate_contam_in_prok_hit_features/feats> ;
        cwl:run     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/generate_fscr_feats.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/blastdb> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/max_target_seqs>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#max_target_seqs> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs>
        cwl:in   <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/input_path> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/num_partitions> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output_glob> ;
        cwl:out  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_make_outputs/output_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_make_outputs.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/fscr_calls_pass1.cwl#repeat_threshold>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-repeat-threshold" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/contam_in_prok_blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/hits>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Create_Adaptor_BLASTdb/title>
        sld:default  "BLASTdb created by GPipe" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_find_frequent_sas.cwl#align_find_frequent/row>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-row" ] ;
        sld:default       1 ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/best_hit_score_edge>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#best_hit_score_edge> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gp_makeblastdb.cwl#asnt>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/label_suffix>
        sld:default  "Adaptor" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/word_size>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#word_size> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "${ 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
                          ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/subject_allowlist>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Find_Frequent_contam_in_prok_Hits/frequent> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastn_wnode/dust>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#dust> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/adaptor_fasta> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/gpx_qdump/unzip>
        sld:default  "*" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/blastdb>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#blastdb> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/adaptor_fasta>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/hits>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/foreign_screening.cwl#foreign_screening/Align_To_Adaptor/hits> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/progs/screen_evaluate.cwl#tab>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-tab" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass>
        rdfs:comment  "corresponds to part of default plane in foreign contamination screening graph of classic Gpipe it should go _after_ all screenings, so it goes to a separate degenerate \"plane\" = \"task\" here" ;
        cwl:in        <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/input> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/asn_cache> ;
        cwl:out       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/calls> ;
        cwl:run       <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/align_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:itemSeparator
                                    "," ;
                            CommandLineBinding:prefix  "-asn-cache"
                          ] ;
        sld:type          [ sld:items  cwl:Directory ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/progs/gpx_qsubmit.cwl#max_batch_length>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max-batch-length" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/generate_fscr_feats/o>
        sld:default  "fscr_feats.asn" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/bacterial_screening.cwl#bacterial_screening/Filter_contam_in_prok_BLAST_Results/filter>
        sld:default  " (align_length >= 50 && pct_identity_gap >= 98) || (align_length >= 100 && pct_identity_gap >= 94) || (align_length >= 200 && pct_identity_gap >= 90)" .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_format_calls/calls>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_fscr_calls_pass1.cwl#fscr_calls_pass1/calls> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/FSCR_Calls_first_pass/input>
        cwl:source  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/bacterial_screening/feats> , <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats> .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_univec_wnode.cwl#tt_univec_wnode/blastdb>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/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/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/out_cache_dir>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir> ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8fb4ac7f5a66897206c7469101a471108b06eada/task_types/tt_blastn_wnode.cwl#gpx_qsubmit/nogenbank>
        sld:default  true .