{"@id":"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"f225cd99b0e0a5043dd102f8b33a6139fefe9ea4","path":"genomic_source/wf_genomic_source.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","url":"https://github.com/ncbi/pgap/blob/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl"},"retrievedOn":"2026-09-21T00:12:13.742+00:00","lastCommit":"f225cd99b0e0a5043dd102f8b33a6139fefe9ea4","label":"Create Genomic Collection for Bacterial Pipeline","inputs":{"fasta":{"type":"File"},"taxid":{"type":"Integer"},"taxon_db":{"type":"File"},"gc_assm_name":{"type":"String"},"submit_block_template":{"type":"File"}},"outputs":{"ids_out":{"type":"File"},"asncache":{"type":"Directory"},"seqid_list":{"type":"File"},"gencoll_asn":{"type":"File"},"stats_report":{"type":"File"}},"steps":{"Cache_FASTA_Sequences":{"label":"prime_cache","run":"../progs/prime_cache.cwl","runType":"COMMANDLINETOOL","sources":{"Cache_FASTA_Sequences":{"sourceIDs":["taxon_db"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Cache_FASTA_Sequences/input":{"sourceIDs":["fasta"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Cache_FASTA_Sequences/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Cache_FASTA_Sequences/submit_block_template":{"sourceIDs":["submit_block_template"]}}},"Extract_Assembly_Information":{"label":"Extract Assembly Information I","run":"gc_get_molecules.cwl","runType":"COMMANDLINETOOL","sources":{"Extract_Assembly_Information":{"sourceIDs":["Create_Assembly_From_Sequences"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Extract_Assembly_Information/filter":{"defaultVal":"\\\"reference-no-organelle\\\""},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Extract_Assembly_Information/outfile":{"defaultVal":"\\\"ref_no_organelle.gi\\\""}}},"Create_Assembly_From_Sequences":{"label":"Create Assembly From Sequences","run":"gc_create.cwl","runType":"COMMANDLINETOOL","sources":{"Create_Assembly_From_Sequences":{"sourceIDs":["Cache_FASTA_Sequences"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Create_Assembly_From_Sequences/asn_cache":{"sourceIDs":["Cache_FASTA_Sequences"]},"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl#Create_Assembly_From_Sequences/gc_assm_name":{"sourceIDs":["gc_assm_name"]}}},"Extract_Assembly_Information_XML":{"label":"Extract Assembly Information II","run":"gc_asm_xml_description.cwl","runType":"COMMANDLINETOOL","sources":{"Extract_Assembly_Information_XML":{"sourceIDs":["Create_Assembly_From_Sequences"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"taxon_db\" [fillcolor=\"#94DDF4\",label=\"taxon_db\"];\n    \"taxid\" [fillcolor=\"#94DDF4\",label=\"taxid\"];\n    \"submit_block_template\" [fillcolor=\"#94DDF4\",label=\"submit_block_template\"];\n    \"gc_assm_name\" [fillcolor=\"#94DDF4\",label=\"gc_assm_name\"];\n    \"fasta\" [fillcolor=\"#94DDF4\",label=\"fasta\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"seqid_list\" [fillcolor=\"#94DDF4\",label=\"seqid_list\"];\n    \"ids_out\" [fillcolor=\"#94DDF4\",label=\"ids_out\"];\n    \"gencoll_asn\" [fillcolor=\"#94DDF4\",label=\"gencoll_asn\"];\n    \"asncache\" [fillcolor=\"#94DDF4\",label=\"asncache\"];\n    \"stats_report\" [fillcolor=\"#94DDF4\",label=\"stats_report\"];\n  }\n  \"Cache_FASTA_Sequences\" [label=\"prime_cache\"];\n  \"Extract_Assembly_Information\" [label=\"Extract Assembly Information I\"];\n  \"Create_Assembly_From_Sequences\" [label=\"Create Assembly From Sequences\"];\n  \"Extract_Assembly_Information_XML\" [label=\"Extract Assembly Information II\"];\n  \"taxon_db\" -> \"Cache_FASTA_Sequences\" [label=\"taxon_db\"];\n  \"taxid\" -> \"Cache_FASTA_Sequences\" [label=\"taxid\"];\n  \"submit_block_template\" -> \"Cache_FASTA_Sequences\" [label=\"submit_block_template\"];\n  \"fasta\" -> \"Cache_FASTA_Sequences\" [label=\"input\"];\n  \"Create_Assembly_From_Sequences\" -> \"Extract_Assembly_Information\" [label=\"gc_assembly\"];\n  \"default1\" -> \"Extract_Assembly_Information\" [label=\"filter\"];\n  \"default1\" [label=\"\\\"reference-no-organelle\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default2\" -> \"Extract_Assembly_Information\" [label=\"outfile\"];\n  \"default2\" [label=\"\\\"ref_no_organelle.gi\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Cache_FASTA_Sequences\" -> \"Create_Assembly_From_Sequences\" [label=\"unplaced\"];\n  \"gc_assm_name\" -> \"Create_Assembly_From_Sequences\" [label=\"gc_assm_name\"];\n  \"Cache_FASTA_Sequences\" -> \"Create_Assembly_From_Sequences\" [label=\"asn_cache\"];\n  \"Create_Assembly_From_Sequences\" -> \"Extract_Assembly_Information_XML\" [label=\"asnfile\"];\n  \"Extract_Assembly_Information\" -> \"seqid_list\";\n  \"Cache_FASTA_Sequences\" -> \"ids_out\";\n  \"Create_Assembly_From_Sequences\" -> \"gencoll_asn\";\n  \"Cache_FASTA_Sequences\" -> \"asncache\";\n  \"Extract_Assembly_Information_XML\" -> \"stats_report\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/genomic_source/wf_genomic_source.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/f225cd99b0e0a5043dd102f8b33a6139fefe9ea4/LICENSE.md"}