{"@id":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","path":"bacterial_annot/wf_bacterial_annot_pass4.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","url":"https://github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl"},"retrievedOn":"2026-08-30T10:23:35.728+00:00","lastCommit":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","label":"Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)","inputs":{"lds2":{"type":"File"},"taxid":{"type":"Integer"},"CDDdata":{"type":"Directory"},"blastdb":{"label":"Input blastdb 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\"Find_Naming_Protein_Hits\" [label=\"blastdb_dir\"];\n  \"taxon_db\" -> \"Find_Naming_Protein_Hits\" [label=\"taxon_db\"];\n  \"genus_list\" -> \"Find_Naming_Protein_Hits\" [label=\"genus_list\"];\n  \"Good_AntiFam_filtered_proteins_gilist\" -> \"Find_Naming_Protein_Hits\" [label=\"ids\"];\n  \"naming_sqlite\" -> \"Add_Names_to_Proteins\" [label=\"unicoll_sqlite\"];\n  \"annotation\" -> \"Add_Names_to_Proteins\" [label=\"input\"];\n  \"Assign_SPARCL_Architecture_Names_to_Proteins_sparclbl\" -> \"Add_Names_to_Proteins\" [label=\"proteins\"];\n  \"wp_assignments\" -> \"Add_Names_to_Proteins\" [label=\"proteins\"];\n  \"hmm_assignments\" -> \"Add_Names_to_Proteins\" [label=\"proteins\"];\n  \"Assign_Clusters_to_Proteins\" -> \"Add_Names_to_Proteins\" [label=\"proteins\"];\n  \"sequence_cache\" -> \"Add_Names_to_Proteins\" [label=\"asn_cache\"];\n  \"defline_cleanup_rules\" -> \"Add_Names_to_Proteins\" [label=\"defline_cleanup_rules\"];\n  \"Add_Names_to_Proteins\" -> \"Bacterial_Annot_Filter\" [label=\"input\"];\n  \"thresholds\" -> \"Bacterial_Annot_Filter\" [label=\"thr\"];\n  \"sequence_cache\" -> \"Bacterial_Annot_Filter\" [label=\"asn_cache\"];\n  \"sequence_cache\" -> \"Assign_Clusters_to_Proteins\" [label=\"asn_cache\"];\n  \"uniColl_cache\" -> \"Assign_Clusters_to_Proteins\" [label=\"asn_cache\"];\n  \"identification_db_dir\" -> \"Assign_Clusters_to_Proteins\" [label=\"namedb_dir\"];\n  \"lds2\" -> \"Assign_Clusters_to_Proteins\" [label=\"lds2\"];\n  \"naming_sqlite\" -> \"Assign_Clusters_to_Proteins\" [label=\"unicoll_sqlite\"];\n  \"proteins\" -> \"Assign_Clusters_to_Proteins\" [label=\"proteins\"];\n  \"Assign_Clusters_to_Proteins_sort\" -> \"Assign_Clusters_to_Proteins\" [label=\"hits\"];\n  \"sequence_cache\" -> \"Find_best_protein_hits\" [label=\"asn_cache\"];\n  \"uniColl_cache\" -> \"Find_best_protein_hits\" [label=\"asn_cache\"];\n  \"Find_Naming_Protein_Hits\" -> \"Find_best_protein_hits\" [label=\"input\"];\n  \"lds2\" -> \"Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences\" [label=\"lds2\"];\n  \"proteins\" -> \"Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences\" [label=\"proteins\"];\n  \"Prepare_SPARCLBL_input\" -> \"Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences\" [label=\"input\"];\n  \"Find_best_protein_hits\" -> \"Assign_Clusters_to_Proteins_sort\" [label=\"input\"];\n  \"Assign_SPARCL_Architecture_Names_to_Proteins_gp_fetch_sequences\" -> \"Assign_SPARCL_Architecture_Names_to_Proteins_asn2fasta\" [label=\"i\"];\n  \"Bacterial_Annot_Filter\" -> \"out_annotation\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_annot/wf_bacterial_annot_pass4.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md"}