@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix Dirent: <https://w3id.org/cwl/cwl#Dirent/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "BLAST against rRNA db, gather" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-unzip" "*" "-num-partitions" "1" ) ;
        cwl:arguments            ( "-unzip" "*" "-num-partitions" "1" ) ;
        cwl:baseCommand          ( "gpx_make_outputs" ) ;
        cwl:baseCommand          ( "gpx_make_outputs" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#output_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#input_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#blast_align> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#23s_blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run genomic CMsearch (5S rRNA), scatter" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#output> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/rfam_stockholm>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_stockholm> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#rfam_stockholm>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-rfam-stockholm" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/rfam_amendments>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_amendments> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Post-process CMsearch annotations" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-unique" ) ;
        cwl:baseCommand          ( "annot_merge" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#output_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#input> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#annots> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/outname> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/product_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/blastdb_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/annotations> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/product_name>
        cwl:default  "23S ribosomal RNA" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/alignments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/blastdb_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/aligns> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/annots> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#output_dir>
        cwl:default       "output" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump/annots> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdb" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdb" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#seqids> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "BLAST against rRNA db, execution" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-evalue" "0.01" "-max_target_seqs" "250" "-soft_masking" "true" "-task" "blastn" "-word_size" "12" "-swap-rows" ) ;
        cwl:arguments            ( "-evalue" "0.01" "-max_target_seqs" "250" "-soft_masking" "true" "-task" "blastn" "-word_size" "12" "-swap-rows" ) ;
        cwl:baseCommand          ( "blastn_wnode" ) ;
        cwl:baseCommand          ( "blastn_wnode" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#output_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#outdir> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/jobs> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#annots>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/annots> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#23s_blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_amendments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/annotation>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#outname> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/outname>
        cwl:default  "annotations_23s.asn" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#blastdb_dir>
        sld:type  cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#16s_blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#output>
        cwl:default       "jobs.xml" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#seqids> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Run genomic CMsearch (5S rRNA)" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_stockholm> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#model_path> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#taxon_db> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_amendments> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#annots> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#annots>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#outname>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#output_name>
        cwl:default       "blast.#.asn" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run genomic CMsearch (5S rRNA), gather" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-unzip" "*" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#output_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#input_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#annots> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/outdir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#cmsearch_cpu>
        cwl:default       0 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-cmsearch-cpu" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_23s>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/annotations> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#seqids> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#annotations>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/annotations> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/model_path>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#model_path> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qdump.cwl#output_name>
        cwl:default       "cmsearch.asn" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_5s>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/annots> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/product_name>
        cwl:default  "16S ribosomal RNA" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#16s_blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "BLAST against rRNA db" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#outname> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#product_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#seqids> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#annotations> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#alignments>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdb" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-blastdb" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#model_path>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Generate rRNA Annotation" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-filter-accept" "pct_identity_gap >= 70" "-gap-tolerance" "1000" "-submission-mode-genbank" ) ;
        cwl:arguments            ( "-filter-accept" "pct_identity_gap >= 70" "-gap-tolerance" "1000" "-submission-mode-genbank" ) ;
        cwl:baseCommand          ( "ribosomal_align2annot" ) ;
        cwl:baseCommand          ( "ribosomal_align2annot" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#product_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#annotation> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#alignments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#blastdb> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#annotations> ;
        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:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/alignments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/annotation> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/product_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/annotations> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#annots>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#go>
        sld:type  [ sld:items  xsd:boolean ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/rfam_stockholm>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_stockholm> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#output_dir>
        cwl:default       "output" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S/blastdb>
        cwl:default  "Ribosom23S" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/rfam_amendments>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_amendments> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#alignments>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/outname> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/product_name> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/blastdb_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/annotations> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Run genomic CMsearch (5S rRNA), execution" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "cmsearch_wnode" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#rfam_stockholm> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#cmsearch_path> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#rfam_amendments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#taxon_db> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#model_path> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#cmsearch_cpu> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#output_dir> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#asncache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#outdir> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_submit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/blastdb>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/product_name>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#product_name> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#product_name>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Post_process_CMsearch_annotations_5S_rRNA/input>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump/annots> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#annotation>
        cwl:default       "annotations.asn" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_stockholm>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#rfam_amendments>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-rfam-amendments" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "BLAST against rRNA db, scatter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-affinity" "subject" "-max-batch-length" "50000" ) ;
        cwl:arguments            ( "-affinity" "subject" "-max-batch-length" "50000" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#output> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#jobs> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#seqids> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/alignments>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs/blast_align> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#output_name>
        cwl:default       "annots.asn" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#output>
        cwl:default       "jobs.xml" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#annotations>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.annotation)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.annotation)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#cmsearch_path>
        cwl:default       "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-cmsearch-path" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/outname>
        cwl:default  "annotations_16s.asn" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_make_outputs/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#model_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-model-path" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#seqids> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_16s>
        cwl:outputSource  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/annotations> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#output>
        cwl:default       "align.asn" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/taxon_db> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/rfam_stockholm> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/model_path> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/rfam_amendments> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S/annots> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_amendments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#model_path>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_make_outputs.cwl#blast_align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blast.*.asn" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blast.*.asn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/annot_merge.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/alignments>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Merge_nS_rRNA_Alignments/aligns> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_dump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/outdir> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Non-Coding Bacterial Genes" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_23S> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_5S> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#23s_blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#taxon_db> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#model_path> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_stockholm> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#16s_blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#rfam_amendments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#go> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_23s> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_16s> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#annotations_5s> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#aligns>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#asncache>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.asn_cache.basename)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/model_path>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#model_path> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/rfam_amendments> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/taxon_db> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/rfam_stockholm> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/input_jobs> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/model_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#Run_genomic_CMsearch_5S_rRNA_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/ribosomal_align2annot.cwl#product_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-product-name" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-product-name" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_bacterial_noncoding.cwl#bacterial_noncoding_16S/blastdb>
        cwl:default  "blastdb" .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/cmsearch_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#rfam_stockholm>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_gcmsearch.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/input_jobs> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_blastn_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/blastn_wnode.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Merge rRNA Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-filter" "align_length >= 60" "-ifmt" "seq-align-set" "-max-discontinuity" "20" "-collated" "-compart" "-fill-gaps" ) ;
        cwl:arguments            ( "-filter" "align_length >= 60" "-ifmt" "seq-align-set" "-max-discontinuity" "20" "-collated" "-compart" "-fill-gaps" ) ;
        cwl:baseCommand          ( "align_merge" ) ;
        cwl:baseCommand          ( "align_merge" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#asn_cache> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#output> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#alignments> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/align_merge.cwl#aligns> ;
        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:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/blastdb> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/seqids> , <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#BLAST_against_nS_rRNA_db_gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_blastn.cwl> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#Generate_nS_rRNA_Annotation/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/wf_blastn.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/8a8fffb78b1e327ba0da51840ac8acc0c218d611/bacterial_noncoding/gpx_qsubmit_gcmsearch.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .