{"@id":"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"4def84df33963fc9ac9d5c5f804b911d01a0d9ad","path":"bacterial_ncrna/wf_gcmsearch.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","url":"https://github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl"},"retrievedOn":"2026-09-27T08:12:36.925+00:00","lastCommit":"4def84df33963fc9ac9d5c5f804b911d01a0d9ad","label":"Run genomic CMsearch (Rfam rRNA)","inputs":{"go":{"type":"Boolean[]"},"seqids":{"type":"File"},"taxon_db":{"type":"File"},"asn_cache":{"type":"Directory"},"model_path":{"type":"File"},"rfam_stockholm":{"type":"File"},"rfam_amendments":{"type":"File"}},"outputs":{"annots":{"type":"File"}},"steps":{"Run_genomic_CMsearch_Rfam_rRNA_wnode":{"label":"Run genomic CMsearch (Rfam rRNA), execution","run":"cmsearch_wnode.cwl","runType":"COMMANDLINETOOL","sources":{"Run_genomic_CMsearch_Rfam_rRNA_wnode":{"sourceIDs":["asn_cache"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_wnode/taxon_db":{"sourceIDs":["taxon_db"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_wnode/input_jobs":{"sourceIDs":["Run_genomic_CMsearch_Rfam_rRNA_submit"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_wnode/model_path":{"sourceIDs":["model_path"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_wnode/rfam_stockholm":{"sourceIDs":["rfam_stockholm"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_wnode/rfam_amendments":{"sourceIDs":["rfam_amendments"]}}},"Run_genomic_CMsearch_Rfam_rRNA_submit":{"label":"Run genomic CMsearch (Rfam rRNA), scatter","run":"gpx_qsubmit.cwl","runType":"COMMANDLINETOOL","sources":{"Run_genomic_CMsearch_Rfam_rRNA_submit":{"sourceIDs":["seqids"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Run_genomic_CMsearch_Rfam_rRNA_submit/asn_cache":{"sourceIDs":["asn_cache"]}}},"Post_process_CMsearch_Rfam_annotations":{"label":"Post-process CMsearch annotations","run":"annot_merge.cwl","runType":"COMMANDLINETOOL","sources":{"Post_process_CMsearch_Rfam_annotations":{"sourceIDs":["Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl#Post_process_CMsearch_Rfam_annotations/asn_cache":{"sourceIDs":["asn_cache"]}}},"Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump":{"label":"Run genomic CMsearch (Rfam rRNA), gather","run":"gpx_qdump.cwl","runType":"COMMANDLINETOOL","sources":{"Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump":{"sourceIDs":["Run_genomic_CMsearch_Rfam_rRNA_wnode"]}}}},"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    \"asn_cache\" [fillcolor=\"#94DDF4\",label=\"asn_cache\"];\n    \"model_path\" [fillcolor=\"#94DDF4\",label=\"model_path\"];\n    \"taxon_db\" [fillcolor=\"#94DDF4\",label=\"taxon_db\"];\n    \"rfam_amendments\" [fillcolor=\"#94DDF4\",label=\"rfam_amendments\"];\n    \"rfam_stockholm\" [fillcolor=\"#94DDF4\",label=\"rfam_stockholm\"];\n    \"seqids\" [fillcolor=\"#94DDF4\",label=\"seqids\"];\n    \"go\" [fillcolor=\"#94DDF4\",label=\"go\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"annots\" [fillcolor=\"#94DDF4\",label=\"annots\"];\n  }\n  \"Run_genomic_CMsearch_Rfam_rRNA_submit\" [label=\"Run genomic CMsearch (Rfam rRNA), scatter\"];\n  \"Post_process_CMsearch_Rfam_annotations\" [label=\"Post-process CMsearch annotations\"];\n  \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"Run genomic CMsearch (Rfam rRNA), execution\"];\n  \"Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump\" [label=\"Run genomic CMsearch (Rfam rRNA), gather\"];\n  \"seqids\" -> \"Run_genomic_CMsearch_Rfam_rRNA_submit\" [label=\"seqids\"];\n  \"asn_cache\" -> \"Run_genomic_CMsearch_Rfam_rRNA_submit\" [label=\"asn_cache\"];\n  \"Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump\" -> \"Post_process_CMsearch_Rfam_annotations\" [label=\"input\"];\n  \"asn_cache\" -> \"Post_process_CMsearch_Rfam_annotations\" [label=\"asn_cache\"];\n  \"asn_cache\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"asn_cache\"];\n  \"rfam_amendments\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"rfam_amendments\"];\n  \"rfam_stockholm\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"rfam_stockholm\"];\n  \"model_path\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"model_path\"];\n  \"Run_genomic_CMsearch_Rfam_rRNA_submit\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"input_jobs\"];\n  \"taxon_db\" -> \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" [label=\"taxon_db\"];\n  \"Run_genomic_CMsearch_Rfam_rRNA_wnode\" -> \"Run_genomic_CMsearch_Rfam_rRNA_Run_genomic_CMsearch_Rfam_rRNA_dump\" [label=\"input_path\"];\n  \"Post_process_CMsearch_Rfam_annotations\" -> \"annots\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/bacterial_ncrna/wf_gcmsearch.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/LICENSE.md"}