@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 ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/input>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_impl)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/k>
        sld:default  5 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#outc>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--outc" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--outc" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#superkingdom>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-superkingdom" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#sorted_seeds>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-i" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#max_extent>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-max_extent" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#compartments>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#group>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-group" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "miniprot" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "miniprot" ) ;
        cwl:baseCommand          ( "miniprot" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#proteins> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#n> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#L> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#genome> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#G> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#e> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#T> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#outs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#p> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#B> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#stdout_redir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#l> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#N> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#outc> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#cpu_count> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#S> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#paf> ;
        cwl:stdout               "$(inputs.stdout_redir)" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#group>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-group" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#fasta>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#G>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-G" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-G" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#input_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/action> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/delta_seqs_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/generic_output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/gilist> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/delta_seqs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/generic_output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/cpu_count>
        sld:default  16 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#subject_allowlist_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-subject-allowlist" ] ;
        sld:default       "subject_allowlist.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#onon_match_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#input> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#filter> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#input_mft> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#subject_allowlist_mft> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#o_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#compartments_mft> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#subject_allowlist> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#onon_match> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#o> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# subject_allowlist.mft created for align_filter from input \"subject_allowlist\" File\\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\\n';  return blob; }}" ;
                                                  cwl:entryname  "subject_allowlist.mft"
                                                ] ;
                                   cwl:listing  [ cwl:entry      "${\n  var blob = '# compartments.mft created for align_filter from input \"compartments\" Array of Files\\n';\n  if (inputs.compartments) {  \n    for (var i = 0; i < inputs.compartments.length; i++) {\n      blob += inputs.compartments[i].path + '\\n';\n    }\n  }\n  return blob;\n}\n" ;
                                                  cwl:entryname  "compartments.mft"
                                                ] ;
                                   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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#filter_accept>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-filter-accept" ] ;
        sld:default       "pct_coverage = 100 AND qframe = 0 AND sframe = 0 AND cds_internal_stops = 0" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#genome>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/k>
        sld:default  "query,subject,-score,cigar" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/taxon_db> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/filter>
        sld:default  "subject_coverage >= 10" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#go>
        sld:type  [ sld:items  xsd:boolean ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/n>
        sld:default  2 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/gencode>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#o>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.o_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/file_in> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#stdout_redir>
        sld:default  "miniprot.paf" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#B>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-B" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-B" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/S>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/seqids>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments/seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#all_prots> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#paf_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "paf.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/ifmt>
        sld:default  "seq-align" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments/aligns> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments/seqids> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/l>
        sld:default  4 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cross_origin_fasta" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "cross_origin_fasta" ) ;
        cwl:baseCommand          ( "cross_origin_fasta" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs_input> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#window> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#action> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#min_pct_ident> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#gilist> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#generic_output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#generic_output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#n>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-n" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-n" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/window>
        sld:default  21 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#db_gencode>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-db_gencode" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "compart_annot2all" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-ofmt" "reference-id" ) ;
        cwl:baseCommand          ( "compart_annot2all" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#seqids_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#aligns> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#seqids> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/p> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/outs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/S> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/T> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/N> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/cpu_count> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/proteins> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/outc> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/genome> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/n> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/L> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/paf> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#gilist>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, gather" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-unzip" "*" "-num-partitions" "1" ) ;
        cwl:baseCommand          ( "gpx_make_outputs" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#input_path> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#paf>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#seqids_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "seqids.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/N>
        sld:default  1000 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#subject_allowlist>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#S>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-S" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-S" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#compartments>
        sld:type  sld:null ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Align reference proteins plane complete workflow, with miniprot" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#all_prots> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#genomic_ids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#go> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxon_db> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#compartments> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#align> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-odelta-seqs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-odelta-seqs" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/file_in>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#all_prots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "protein.fa" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/cpu_count> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/e> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/l> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/outc> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/N> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/p> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/B> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/T> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/S> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/n> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/G> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/genome> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/outs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/L> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/proteins> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/paf> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align_sort" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_sort" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#input_manifest> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#top> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#input> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#group> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#proteins>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "blast.#.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/L>
        sld:default  15 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/T>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/value> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "paf2asn" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-partial-intron-threshold" "100" "-no-scores" "-pack-parts" "-split-introns" "-uniquify" ) ;
        cwl:baseCommand          ( "paf2asn" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#paf> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#paf_manifest> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#align> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# paf.mft created for paf2asn from input paf Array of Files\\n'; for (var i = 0; i < inputs.paf.length; i++) { blob += inputs.paf[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "paf.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#generic_output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.delta_seqs_name)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.delta_seqs_name)" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#N>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-N" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-N" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#filter>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-filter" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Protein Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-filter" "pct_identity_gapopen_only >= 50 AND NOT (pct_coverage < 20 and (query_entropy < 0.3 OR query_seg_pct > 60)) AND ( (query_start<=20 AND SUB(query_length, query_end)<=20) OR pct_identity_gapopen_only >= 60 ) AND (SUB(subject_end, subject_start) > 90 || SUB(subject_end, subject_start) > MUL(query_length,1.5) || num_ident >=60) AND (query_length > 30 || (pct_identity_gap >= 80 AND SUB(subject_end, subject_start) >= MUL(query_length,2.4)))" "-ifmt" "seq-align" "-nogenbank" ) ;
        cwl:baseCommand          ( "align_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output_non_match> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#file_in> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align_non_match> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align_non_match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_non_match)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/min_pct_ident>
        sld:default  3e-01 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#seqids>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align_sort_ma" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "align_sort" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#input_manifest> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#group> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#top> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#input> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#nogenbank> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#nomatch_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-nomatch" ] ;
        sld:default       "no-match" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#seqids_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out" ] ;
        sld:default       "reference_protein.seqids" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/max_extent> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/sorted_seeds> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/filter_accept> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/blast_full_cov> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/blastdb_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Seed Protein Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/ifmt>
        sld:default  "seq-align-set" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/filter_accept>
        sld:default  "pct_coverage >= 70" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#gencode>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-gencode" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blast_align>
        cwl:outputSource  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/blast_align> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#gilist_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:default       "gilist.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/generic_output_name>
        sld:default  "genomic.fa" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/ifmt>
        sld:default  "seq-align" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#cpu_count>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/match> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#k>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:default       true ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/k>
        sld:default  "query subject" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/G>
        sld:default  500 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#nomatch>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.nomatch_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#align>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#T>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-T" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-T" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/p>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#file_in>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#action>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-action" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-action" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/generic_output_name>
        sld:default  "remap_align.asn" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#onon_match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.onon_match_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/value> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#input>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/B>
        sld:default  0 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/outdir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/align>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/max_extent>
        sld:default  100 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/delta_seqs_name>
        sld:default  "delta_sequences.asn" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#seqids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.seqids_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#e>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-e" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-e" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/n>
        sld:default  2 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/input>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/blast_full_cov> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/generic_output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#p>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-p" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-p" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compart_annot2all.cwl#aligns>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/genome>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/generic_output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#input_manifest>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-manifest" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_partial_cov>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.part_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output_impl>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "gencode.txt" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/asn_cache>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, execute" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-align_filter" "pct_identity_gapopen_only >= 75" "-backlog" "1" "-comp_based_stats" "F" "-dbsize" "6000000000" "-delay" "0" "-evalue" "0.1" "-gapextend" "2" "-gapopen" "9" "-matrix" "BLOSUM62" "-max-jobs" "1" "-seg" "no" "-soft_masking" "true" "-threshold" "21" "-word_size" "6" "-nogenbank" "-short-protein-threshold" "30" ) ;
        cwl:baseCommand          ( "tblastn_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#output_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#db_gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#input_jobs> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.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.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  4000
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/S>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Short_Sequences/match> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#delta_seqs_input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-delta-seqs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-delta-seqs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#match>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.match_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#uniColl_asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "compute_gencode" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "compute_gencode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxid> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#superkingdom> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output_impl> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#gencode> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxon_db> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#output> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#k>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/paf>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/paf> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/paf> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#full_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ofull" ] ;
        sld:default       "align_full_cov.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/cpu_count>
        sld:default  16 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#generic_output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.generic_output_name)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.generic_output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#ifmt>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ifmt" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/outs>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxid> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/gilist>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#genomic_ids> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#input>
        cwl:inputBinding  [ cwl:loadContents  true ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/db_gencode>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#db_gencode> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-asn-cache" ;
                            cwl:valueFrom              "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)"
                          ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/N>
        sld:default  1000 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/action>
        sld:default  "create" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#min_pct_ident>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-min-pct-ident" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-min-pct-ident" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/outs>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/db_gencode> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort_ma.cwl#top>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/gilist> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/fasta> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/fasta> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#part_output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-opartial" ] ;
        sld:default       "align_partial_cov.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/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/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/outc>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/compartments>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/seqids> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/action>
        sld:default  "remap" .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/input>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/o> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/outc>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/T>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/value> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "align.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/subject_allowlist>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#all_prots> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "getfasta" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-skip-duplicates" ) ;
        cwl:baseCommand          ( "getfasta" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#gilist> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#gilist_mft> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#fasta> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# gilist.mft created for getfasta from input gilist Array of Files\\n'; for (var i = 0; i < inputs.gilist.length; i++) { blob += inputs.gilist[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "gilist.mft"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments/aligns>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#compartments> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#match_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "match" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/compartments> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/subject_allowlist> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/filter> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Compartments/o> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/genome>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/generic_output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_full_cov>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.full_output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter Full-Coverage Alignments" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-nogenbank" ) ;
        cwl:baseCommand          ( "bacterial_protalign_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#full_output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#sorted_seeds> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#filter_accept> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#max_extent> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#part_output> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_full_cov> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/bacterial_protalign_filter.cwl#blast_partial_cov> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMax  8000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.asn_cache)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#l>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-l" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-l" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#blast_align>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "blast.*.asn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/sorted_seeds>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/output> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/getfasta.cwl#gilist>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#k>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-k" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "seq_filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-filter" "length < 30" ) ;
        cwl:baseCommand          ( "seq_filter" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#nomatch_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#match_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#seqids_mft> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#nomatch> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/seq_filter.cwl#match> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "${var blob = '# seqids.mft created for seq_filter from input seqids Array of Files\\n'; for (var i = 0; i < inputs.seqids.length; i++) { blob += inputs.seqids[i].path + '\\n'; } return blob; }" ;
                                                  cwl:entryname  "seqids.mft"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/paf> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/asn_cache> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Convert_PAF_Alignments/align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb>
        cwl:inputBinding  [ CommandLineBinding:prefix  "-db" ;
                            cwl:valueFrom              "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
                          ] ;
        sld:default       "blastdb" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#genomic_ids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Seed Protein Alignments, scatter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-affinity" "subject" "-max-batch-length" "10000" "-nogenbank" ) ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#output> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb_dir> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#blastdb> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#uniColl_asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_qsubmit_seqids.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.uniColl_asn_cache)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.blastdb_dir)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/L>
        sld:default  15 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Protein_Alignments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_fast/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/fasta> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#paf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.stdout_redir)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.stdout_redir)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/compute_gencode.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl#window>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-window" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-window" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#value>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/e>
        sld:default  500 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/tblastn_wnode_db.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/align> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/delta_seqs_input> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/generic_output_name> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/window> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/action> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/min_pct_ident> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/generic_output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/cross_origin_fasta.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Run_Miniprot_slow/p>
        sld:default  1e-02 .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/paf2asn.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "miniprot.asn" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#outs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--outs" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--outs" ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Short_Protein_Alignments/input>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Align_Short_Proteins/blast_align> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl#top>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-top" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/align_filter.cwl#output_non_match>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-non-match-output" ] ;
        sld:default       "align-nomatch.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/asn_cache> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/ifmt> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/nogenbank> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/k> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Sort_Protein_Alignments/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_sort.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/blastdb_dir>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#blastdb_dir> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_make_outputs/blast_align> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/gpx_make_outputs.cwl> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#gpx_qsubmit/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#seqids> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#tblastn_wnode/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_seed_seqids.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl>
        a                          cwl:ExpressionTool ;
        ns1:original_cwlVersion    "v1.2" ;
        ExpressionTool:expression  "${ return { \"value\": parseInt(inputs.input.contents) }; }\n" ;
        cwl:cwlVersion             cwl:v1.2 ;
        cwl:inputs                 <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#input> ;
        cwl:outputs                <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl#value> ;
        cwl:requirements           [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Remap_cross_origin_alignments/delta_seqs_input>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Genomic_FASTA/delta_seqs> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/align_filter.cwl#compartments_mft>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-compartments-manifest" ] ;
        sld:default       "compartments.mft" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Filter_Full_Coverage_Alignments/uniColl_asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#uniColl_asn_cache> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/miniprot.cwl#L>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-L" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-L" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Get_Protein_FASTA/gilist>
        cwl:linkMerge  "merge_flattened" ;
        cwl:source     <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Extract_Proteins_From_Compartments/seqids> , <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#all_prots> .

<https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int>
        cwl:in   <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/protein_alignment/wf_protein_alignment_miniprot.cwl#Compute_Gencode_int/value> ;
        cwl:run  <https://w3id.org/cwl/view/git/01a5c0a8834846ce04fed190eec7d1cc39a3df48/progs/file2int.cwl> .