{"@id":"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"4533a5e930305c674057bc4cf5dda4f39d39b5df","path":"bacterial_kmer/wf_bacterial_kmer.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl","url":"https://github.com/ncbi/pgap/blob/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl"},"retrievedOn":"2026-09-27T08:10:21.074+00:00","lastCommit":"4533a5e930305c674057bc4cf5dda4f39d39b5df","label":"bacterial_kmer","inputs":{"gc_cache":{"type":"File"},"taxon_db":{"type":"File"},"asn_cache":{"type":"Directory"},"tax_synon":{"type":"File"},"ANI_cutoff":{"type":"File"},"gencoll_asn":{"type":"File"},"gc_seq_cache":{"type":"Directory"},"ref_assembly_id":{"type":"Integer"},"gcextract2_sqlite":{"type":"File"},"kmer_cache_sqlite":{"type":"File"},"ref_assembly_taxid":{"type":"Integer"},"ani_report_transform":{"type":"File"},"kmer_reference_assemblies":{"type":"File"},"Extract_Kmers_From_Input___entry":{"type":"File"}},"outputs":{"Identify_Top_N_ANI_top":{"type":"File"},"Identify_Top_N_ANI_annot":{"type":"File"},"Identify_Top_N_ANI_top_txt":{"type":"File"},"Extract_Top_Assemblies___tax_report":{"type":"File"}},"steps":{"List_sqlite":{"label":"list_kmer_sqlite.cwl","doc":"Produces 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together reference kmer store and newly created kmer store for a new 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= 3 AND align_length_ungap >= 5) OR align_length > 1000) AND pct_identity_gap > 25\\\""},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Assembly_Assembly_BLASTn/queries_gc_id_list":{"sourceIDs":["Extract_Input_GenColl_IDs"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Assembly_Assembly_BLASTn/subjects_gc_id_list":{"sourceIDs":["Extract_Top_Assemblies"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Assembly_Assembly_BLASTn/use_common_components":{"defaultVal":"true"}}},"Extract_Kmers_From_Input":{"label":"kmer_seq_entry_extract_wnode","run":"../task_types/tt_kmer_seq_entry_extract_wnode.cwl","runType":"WORKFLOW","sources":{"Extract_Kmers_From_Input":{"sourceIDs":["asn_cache"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Extract_Kmers_From_Input/entry":{"sourceIDs":["Extract_Kmers_From_Input___entry"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Extract_Kmers_From_Input/kmer_file_list":{"sourceIDs":["kmer_reference_assemblies"]}}},"Extract_Input_GenColl_IDs":{"label":"gc_extract_ids","run":"../progs/gc_extract_ids.cwl","runType":"COMMANDLINETOOL","sources":{"Extract_Input_GenColl_IDs":{"sourceIDs":["gencoll_asn"]}}},"Convert_kmer_files_to_sqlite":{"label":"kmer_files2sqlite.cwl","doc":"Convert input .kmer.gz (kmer_file) and .xml (kmer_metadata_file)\ninto new sqlite database\nTakes a directory input\n","run":"../progs/kmer_files2sqlite.cwl","runType":"COMMANDLINETOOL","sources":{"Convert_kmer_files_to_sqlite":{"sourceIDs":["Extract_Kmers_From_Input"]}}},"Identify_Top_N_ANI_transform":{"label":"xsltproc","run":"../progs/xsltproc.cwl","runType":"COMMANDLINETOOL","sources":{"Identify_Top_N_ANI_transform":{"sourceIDs":["ani_report_transform"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Identify_Top_N_ANI_transform/xml":{"sourceIDs":["Identify_Top_N_ANI"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Identify_Top_N_ANI_transform/output_name":{"defaultVal":"\\\"ani-tax-report.txt\\\""}}},"Get_Top_Assemblies_GenColl_ASN":{"label":"gcaccess_from_list","run":"../task_types/tt_gcaccess_from_list.cwl","runType":"WORKFLOW","sources":{"Get_Top_Assemblies_GenColl_ASN":{"sourceIDs":["Extract_Top_Assemblies"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Get_Top_Assemblies_GenColl_ASN/gc_cache":{"sourceIDs":["gc_cache"]}}},"Compare_Kmer_Pairwise_prepare_input":{"doc":"concatenates input File[] to output File","run":"../progs/cat.cwl","runType":"COMMANDLINETOOL","sources":{"Compare_Kmer_Pairwise_prepare_input":{"sourceIDs":["List_sqlite"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Compare_Kmer_Pairwise_prepare_input/input":{"sourceIDs":["Identify_Top_N"]},"https://w3id.org/cwl/view/git/4533a5e930305c674057bc4cf5dda4f39d39b5df/bacterial_kmer/wf_bacterial_kmer.cwl#Compare_Kmer_Pairwise_prepare_input/output_file_name":{"defaultVal":"\\\"target_and_matches.ids\\\""}}}},"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    \"gc_cache\" [fillcolor=\"#94DDF4\",label=\"gc_cache\"];\n    \"ref_assembly_id\" [fillcolor=\"#94DDF4\",label=\"ref_assembly_id\"];\n    \"ref_assembly_taxid\" [fillcolor=\"#94DDF4\",label=\"ref_assembly_taxid\"];\n    \"asn_cache\" [fillcolor=\"#94DDF4\",label=\"asn_cache\"];\n    \"kmer_reference_assemblies\" [fillcolor=\"#94DDF4\",label=\"kmer_reference_assemblies\"];\n    \"kmer_cache_sqlite\" [fillcolor=\"#94DDF4\",label=\"kmer_cache_sqlite\"];\n    \"ANI_cutoff\" [fillcolor=\"#94DDF4\",label=\"ANI_cutoff\"];\n    \"gcextract2_sqlite\" [fillcolor=\"#94DDF4\",label=\"gcextract2_sqlite\"];\n    \"taxon_db\" [fillcolor=\"#94DDF4\",label=\"taxon_db\"];\n    \"gc_seq_cache\" [fillcolor=\"#94DDF4\",label=\"gc_seq_cache\"];\n    \"gencoll_asn\" [fillcolor=\"#94DDF4\",label=\"gencoll_asn\"];\n    \"ani_report_transform\" [fillcolor=\"#94DDF4\",label=\"ani_report_transform\"];\n    \"Extract_Kmers_From_Input___entry\" [fillcolor=\"#94DDF4\",label=\"Extract_Kmers_From_Input___entry\"];\n    \"tax_synon\" [fillcolor=\"#94DDF4\",label=\"tax_synon\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"Identify_Top_N_ANI_top\" [fillcolor=\"#94DDF4\",label=\"Identify_Top_N_ANI_top\"];\n    \"Extract_Top_Assemblies___tax_report\" [fillcolor=\"#94DDF4\",label=\"Extract_Top_Assemblies___tax_report\"];\n    \"Identify_Top_N_ANI_annot\" [fillcolor=\"#94DDF4\",label=\"Identify_Top_N_ANI_annot\"];\n    \"Identify_Top_N_ANI_top_txt\" [fillcolor=\"#94DDF4\",label=\"Identify_Top_N_ANI_top_txt\"];\n  }\n  \"Build_Kmer_Tree\" [label=\"kmer_build_tree\", fillcolor=\"#F3CEA1\"];\n  \"Compare_Kmer\" [label=\"kmer_ref_compare_wnode\", fillcolor=\"#F3CEA1\"];\n  \"Assembly_Assembly_BLASTn\" [label=\"assm_assm_blastn_wnode\", fillcolor=\"#F3CEA1\"];\n  \"List_sqlite\" [label=\"list_kmer_sqlite.cwl\"];\n  \"Combine_kmer_sqlite\" [label=\"combine_kmer_sqlite.cwl\"];\n  \"Extract_Kmers_From_Input\" [label=\"kmer_seq_entry_extract_wnode\", fillcolor=\"#F3CEA1\"];\n  \"Identify_Top_N\" [label=\"Identify_Top_N\", fillcolor=\"#F3CEA1\"];\n  \"Convert_kmer_files_to_sqlite\" [label=\"kmer_files2sqlite.cwl\"];\n  \"Identify_Top_N_ANI_transform\" [label=\"xsltproc\"];\n  \"Extract_Input_GenColl_IDs\" [label=\"gc_extract_ids\"];\n  \"Identify_Top_N_ANI\" [label=\"ani_top_n\", fillcolor=\"#F3CEA1\"];\n  \"Extract_Top_Assemblies\" [label=\"kmer_top_n_extract\", fillcolor=\"#F3CEA1\"];\n  \"Get_Top_Assemblies_GenColl_ASN\" [label=\"gcaccess_from_list\", fillcolor=\"#F3CEA1\"];\n  \"Compare_Kmer__Pairwise_\" [label=\"tt_kmer_compare_wnode\", fillcolor=\"#F3CEA1\"];\n  \"Compare_Kmer_Pairwise_prepare_input\" [label=\"Compare_Kmer_Pairwise_prepare_input\"];\n  \"default1\" -> \"Build_Kmer_Tree\" [label=\"sort\"];\n  \"default1\" [label=\"\\\"leaf-count-ascending\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default2\" -> \"Build_Kmer_Tree\" [label=\"skip_markup\"];\n  \"default2\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default3\" -> \"Build_Kmer_Tree\" [label=\"no_merge\"];\n  \"default3\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"Compare_Kmer__Pairwise_\" -> \"Build_Kmer_Tree\" [label=\"distances\"];\n  \"default4\" -> \"Compare_Kmer\" [label=\"dist_method\"];\n  \"default4\" [label=\"\\\"minhash\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Combine_kmer_sqlite\" -> \"Compare_Kmer\" [label=\"kmer_cache_sqlite\"];\n  \"default5\" -> \"Compare_Kmer\" [label=\"score_method\"];\n  \"default5\" [label=\"\\\"boolean\\\"\", fillcolor=\"#D5AEFC\"];\n  \"List_sqlite\" -> \"Compare_Kmer\" [label=\"kmer_list\"];\n  \"kmer_reference_assemblies\" -> \"Compare_Kmer\" [label=\"ref_kmer_list\"];\n  \"default6\" -> \"Compare_Kmer\" [label=\"minhash_signature\"];\n  \"default6\" [label=\"\\\"minhash\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default7\" -> \"Assembly_Assembly_BLASTn\" [label=\"task\"];\n  \"default7\" [label=\"\\\"megablast\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default8\" -> \"Assembly_Assembly_BLASTn\" [label=\"workers_per_cpu\"];\n  \"default8\" [label=\"4e-01\", fillcolor=\"#D5AEFC\"];\n  \"Extract_Top_Assemblies\" -> \"Assembly_Assembly_BLASTn\" [label=\"subjects_gc_id_list\"];\n  \"default9\" -> \"Assembly_Assembly_BLASTn\" [label=\"compart\"];\n  \"default9\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default10\" -> \"Assembly_Assembly_BLASTn\" [label=\"gapextend\"];\n  \"default10\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"Get_Top_Assemblies_GenColl_ASN\" -> \"Assembly_Assembly_BLASTn\" [label=\"ref_gencoll_asn\"];\n  \"default11\" -> \"Assembly_Assembly_BLASTn\" [label=\"window_size\"];\n  \"default11\" [label=\"150\", fillcolor=\"#D5AEFC\"];\n  \"gc_cache\" -> \"Assembly_Assembly_BLASTn\" [label=\"gc_cache\"];\n  \"default12\" -> \"Assembly_Assembly_BLASTn\" [label=\"merge_align_filter\"];\n  \"default12\" [label=\"\\\"((reciprocity = 3 AND align_length_ungap >= 5) OR align_length > 1000) AND pct_identity_gap > 25\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default13\" -> \"Assembly_Assembly_BLASTn\" [label=\"max_target_seqs\"];\n  \"default13\" [label=\"250\", fillcolor=\"#D5AEFC\"];\n  \"default14\" -> \"Assembly_Assembly_BLASTn\" [label=\"max_bases_per_call\"];\n  \"default14\" [label=\"500000000\", fillcolor=\"#D5AEFC\"];\n  \"default15\" -> \"Assembly_Assembly_BLASTn\" [label=\"gapopen\"];\n  \"default15\" [label=\"2\", fillcolor=\"#D5AEFC\"];\n  \"default16\" -> \"Assembly_Assembly_BLASTn\" [label=\"affinity\"];\n  \"default16\" [label=\"\\\"subject\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default17\" -> \"Assembly_Assembly_BLASTn\" [label=\"soft_masking\"];\n  \"default17\" [label=\"\\\"true\\\"\", fillcolor=\"#D5AEFC\"];\n  \"asn_cache\" -> \"Assembly_Assembly_BLASTn\" [label=\"asn_cache\"];\n  \"default18\" -> \"Assembly_Assembly_BLASTn\" [label=\"use_common_components\"];\n  \"default18\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default19\" -> \"Assembly_Assembly_BLASTn\" [label=\"merge_engine\"];\n  \"default19\" [label=\"\\\"tree-merger\\\"\", fillcolor=\"#D5AEFC\"];\n  \"gc_seq_cache\" -> \"Assembly_Assembly_BLASTn\" [label=\"gc_seq_cache\"];\n  \"gencoll_asn\" -> \"Assembly_Assembly_BLASTn\" [label=\"gencoll_asn\"];\n  \"default20\" -> \"Assembly_Assembly_BLASTn\" [label=\"evalue\"];\n  \"default20\" [label=\"1e-04\", fillcolor=\"#D5AEFC\"];\n  \"default21\" -> \"Assembly_Assembly_BLASTn\" [label=\"word_size\"];\n  \"default21\" [label=\"28\", fillcolor=\"#D5AEFC\"];\n  \"Extract_Input_GenColl_IDs\" -> \"Assembly_Assembly_BLASTn\" [label=\"queries_gc_id_list\"];\n  \"Convert_kmer_files_to_sqlite\" -> \"List_sqlite\" [label=\"kmer_cache_sqlite\"];\n  \"default22\" -> \"Combine_kmer_sqlite\" [label=\"fast\"];\n  \"default22\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"kmer_cache_sqlite\" -> \"Combine_kmer_sqlite\" [label=\"kmer_cache_sqlite\"];\n  \"Convert_kmer_files_to_sqlite\" -> \"Combine_kmer_sqlite\" [label=\"kmer_cache_sqlite\"];\n  \"asn_cache\" -> \"Extract_Kmers_From_Input\" [label=\"asn_cache\"];\n  \"kmer_reference_assemblies\" -> \"Extract_Kmers_From_Input\" [label=\"kmer_file_list\"];\n  \"Extract_Kmers_From_Input___entry\" -> \"Extract_Kmers_From_Input\" [label=\"entry\"];\n  \"Compare_Kmer\" -> \"Identify_Top_N\" [label=\"distances\"];\n  \"Combine_kmer_sqlite\" -> \"Identify_Top_N\" [label=\"kmer_cache_sqlite\"];\n  \"Extract_Kmers_From_Input\" -> \"Convert_kmer_files_to_sqlite\" [label=\"kmer_dir\"];\n  \"ani_report_transform\" -> \"Identify_Top_N_ANI_transform\" [label=\"xslt\"];\n  \"Identify_Top_N_ANI\" -> \"Identify_Top_N_ANI_transform\" [label=\"xml\"];\n  \"default23\" -> \"Identify_Top_N_ANI_transform\" [label=\"output_name\"];\n  \"default23\" [label=\"\\\"ani-tax-report.txt\\\"\", fillcolor=\"#D5AEFC\"];\n  \"gencoll_asn\" -> \"Extract_Input_GenColl_IDs\" [label=\"input\"];\n  \"Get_Top_Assemblies_GenColl_ASN\" -> \"Identify_Top_N_ANI\" [label=\"ref_gencoll_asn\"];\n  \"ANI_cutoff\" -> \"Identify_Top_N_ANI\" [label=\"ANI_cutoff\"];\n  \"gcextract2_sqlite\" -> \"Identify_Top_N_ANI\" [label=\"gcextract2_sqlite\"];\n  \"taxon_db\" -> \"Identify_Top_N_ANI\" [label=\"taxon_db\"];\n  \"gencoll_asn\" -> \"Identify_Top_N_ANI\" [label=\"gencoll_asn\"];\n  \"Assembly_Assembly_BLASTn\" -> \"Identify_Top_N_ANI\" [label=\"blast_align\"];\n  \"ref_assembly_id\" -> \"Identify_Top_N_ANI\" [label=\"ref_assembly_id\"];\n  \"ref_assembly_taxid\" -> \"Identify_Top_N_ANI\" [label=\"ref_assembly_taxid\"];\n  \"asn_cache\" -> \"Identify_Top_N_ANI\" [label=\"asn_cache\"];\n  \"gc_seq_cache\" -> \"Identify_Top_N_ANI\" [label=\"asn_cache\"];\n  \"tax_synon\" -> \"Identify_Top_N_ANI\" [label=\"tax_synon\"];\n  \"ref_assembly_id\" -> \"Extract_Top_Assemblies\" [label=\"ref_assembly_id\"];\n  \"Identify_Top_N\" -> \"Extract_Top_Assemblies\" [label=\"top_distances\"];\n  \"taxon_db\" -> \"Extract_Top_Assemblies\" [label=\"taxon_db\"];\n  \"gcextract2_sqlite\" -> \"Extract_Top_Assemblies\" [label=\"gcextract2_sqlite\"];\n  \"ref_assembly_taxid\" -> \"Extract_Top_Assemblies\" [label=\"ref_assembly_taxid\"];\n  \"Extract_Top_Assemblies\" -> \"Get_Top_Assemblies_GenColl_ASN\" [label=\"gc_id_list\"];\n  \"gc_cache\" -> \"Get_Top_Assemblies_GenColl_ASN\" [label=\"gc_cache\"];\n  \"default24\" -> \"Compare_Kmer__Pairwise_\" [label=\"minhash_signature\"];\n  \"default24\" [label=\"\\\"minhash\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Compare_Kmer_Pairwise_prepare_input\" -> \"Compare_Kmer__Pairwise_\" [label=\"kmer_list\"];\n  \"Combine_kmer_sqlite\" -> \"Compare_Kmer__Pairwise_\" [label=\"kmer_cache_sqlite\"];\n  \"default25\" -> \"Compare_Kmer__Pairwise_\" [label=\"score_method\"];\n  \"default25\" [label=\"\\\"boolean\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default26\" -> \"Compare_Kmer__Pairwise_\" [label=\"dist_method\"];\n  \"default26\" [label=\"\\\"minhash\\\"\", fillcolor=\"#D5AEFC\"];\n  \"List_sqlite\" -> \"Compare_Kmer_Pairwise_prepare_input\" [label=\"input\"];\n  \"Identify_Top_N\" -> \"Compare_Kmer_Pairwise_prepare_input\" [label=\"input\"];\n  \"default27\" -> \"Compare_Kmer_Pairwise_prepare_input\" [label=\"output_file_name\"];\n  \"default27\" [label=\"\\\"target_and_matches.ids\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Identify_Top_N_ANI\" -> \"Identify_Top_N_ANI_top\";\n  \"Extract_Top_Assemblies\" -> \"Extract_Top_Assemblies___tax_report\";\n  \"Identify_Top_N_ANI\" -> \"Identify_Top_N_ANI_annot\";\n  \"Identify_Top_N_ANI_transform\" -> 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