{"@id":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","path":"wf_common.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","url":"https://github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl"},"retrievedOn":"2026-08-29T23:46:32.567+00:00","lastCommit":"681555881cbdf95a1f4c29f6dc272eb6ca8e4d60","label":"PGAP Pipeline","doc":"PGAP pipeline for external usage, powered via containers","inputs":{"go":{"type":"Boolean[]"},"taxid":{"type":"Integer"},"dbname":{"type":"String (Optional)"},"entries":{"type":"File (Optional)"},"uuid_in":{"type":"File (Optional)"},"make_uuid":{"type":"Boolean (Optional)"},"os_version":{"type":"String (Optional)"},"seq_submit":{"type":"File (Optional)"},"no_internet":{"type":"Boolean (Optional)"},"gc_assm_name":{"type":"String"},"report_usage":{"type":"Boolean"},"locus_tag_prefix":{"type":"String (Optional)"},"ignore_all_errors":{"type":"Boolean (Optional)"},"submol_block_json":{"type":"File"},"supplemental_data":{"type":"Directory"},"blast_hits_cache_data":{"type":"Directory (Optional)"},"scatter_gather_nchunks":{"type":"String"},"xpath_fail_final_asndisc":{"doc":"The default: setting is for standard call of pgap.cwl (for example, from pgap.py)","type":"String (Optional)"},"contact_as_author_possible":{"type":"Boolean (Optional)"},"xpath_fail_initial_asndisc":{"doc":"The default: setting is for standard call of pgap.cwl (for example, from pgap.py)","type":"String (Optional)"},"xpath_fail_final_asnvalidate":{"doc":"The default: setting is for standard call of pgap.cwl (for example, from pgap.py)","type":"String (Optional)"},"xpath_fail_initial_asnvalidate":{"doc":"The default: setting is for standard call of pgap.cwl (for example, from pgap.py)","type":"String (Optional)"}},"outputs":{"gaf":{"type":"File"},"gbk":{"type":"File"},"gff":{"type":"File"},"sqn":{"type":"File"},"gbent":{"type":"File"},"checkm_raw":{"type":"File"},"protein_fasta":{"type":"File (Optional)"},"checkm_results":{"type":"File"},"nucleotide_fasta":{"type":"File (Optional)"},"proc_annot_stats":{"type":"File"},"cds_protein_fasta":{"type":"File (Optional)"},"all_proc_annot_stats":{"type":"File"},"cds_nucleotide_fasta":{"type":"File (Optional)"},"final_asnval_error_diag":{"type":"File (Optional)"},"final_asndisc_error_diag":{"type":"File (Optional)"},"initial_asnval_error_diag":{"type":"File (Optional)"},"initial_asndisc_error_diag":{"type":"File (Optional)"}},"steps":{"checkm":{"label":"checkm","run":"checkm/wf_checkm.cwl","runType":"WORKFLOW","sources":{"checkm":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#checkm/models":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#checkm/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#checkm/checkm_data_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#checkm/filter_for_raw_checkm":{"sourceIDs":["passdata"]}}},"passdata":{"label":"Split input directory into subpath flows","run":"expr/supplemental_data_split_dir.cwl","runType":"EXPRESSIONTOOL","sources":{"passdata":{"sourceIDs":["supplemental_data"]}}},"orfs_hmms":{"label":"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)","run":"bacterial_annot/wf_orf_hmms.cwl","runType":"WORKFLOW","sources":{"orfs_hmms":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/hmm_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/hmms_tab":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/annotation":{"sourceIDs":["ab_initio_antifam"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#orfs_hmms/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"ping_stop":{"label":"pinger","run":"progs/pinger.cwl","runType":"COMMANDLINETOOL","sources":{"ping_stop":{"sourceIDs":["ping_start"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_stop/infile":{"sourceIDs":["Generate_Annotation_Reports_gbk"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_stop/os_version":{"sourceIDs":["os_version"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_stop/report_usage":{"sourceIDs":["report_usage"]}}},"ping_start":{"label":"pinger","run":"progs/pinger.cwl","runType":"COMMANDLINETOOL","sources":{"ping_start":{"sourceIDs":["make_uuid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_start/uuid_in":{"sourceIDs":["uuid_in"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_start/instring":{"sourceIDs":["gc_assm_name"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_start/os_version":{"sourceIDs":["os_version"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ping_start/report_usage":{"sourceIDs":["report_usage"]}}},"Get_Proteins":{"label":"Get Proteins","run":"wf_bacterial_prot_src.cwl","runType":"WORKFLOW","sources":{"Get_Proteins":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Get_Proteins/blastdb_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Get_Proteins/tax_sql_file":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Get_Proteins/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Get_Proteins/uniColl_asn_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Get_Proteins/all_order_specific_blastdb":{"sourceIDs":["Get_Order_Specific_Strings"]}}},"Add_Locus_Tags":{"label":"add_locus_tags","run":"progs/add_locus_tags.cwl","runType":"COMMANDLINETOOL","sources":{"Add_Locus_Tags":{"sourceIDs":["locus_tag_prefix"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Add_Locus_Tags/input":{"sourceIDs":["bacterial_annot_2nd_pass_blastp"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Add_Locus_Tags/dbname":{"sourceIDs":["dbname"]}}},"bacterial_trna":{"label":"Run tRNAScan","run":"bacterial_trna/wf_trnascan.cwl","runType":"WORKFLOW","sources":{"bacterial_trna":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_trna/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_trna/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_trna/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_trna/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_trna/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"genomic_source":{"label":"Create Genomic Collection for Bacterial Pipeline, ASN.1 input","run":"genomic_source/wf_genomic_source_asn.cwl","runType":"WORKFLOW","sources":{"genomic_source":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#genomic_source/entries":{"sourceIDs":["entries"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#genomic_source/seq_submit":{"sourceIDs":["seq_submit"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#genomic_source/gc_assm_name":{"sourceIDs":["ping_start"]}}},"bacterial_ncrna":{"label":"Run genomic CMsearch (Rfam rRNA)","run":"bacterial_ncrna/wf_gcmsearch.cwl","runType":"WORKFLOW","sources":{"bacterial_ncrna":{"sourceIDs":["Prepare_Unannotated_Sequences_asnvalidate_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/seqids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/model_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/rfam_stockholm":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_ncrna/rfam_amendments":{"sourceIDs":["passdata"]}}},"add_checksum_sqn":{"run":"progs/annot_checksum.cwl","runType":"COMMANDLINETOOL","sources":{"add_checksum_sqn":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]}}},"Cache_Entrez_Gene":{"label":"Cache Entrez Gene","run":"cache_entrez_gene.cwl","runType":"COMMANDLINETOOL","sources":{"Cache_Entrez_Gene":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Cache_Entrez_Gene/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Cache_Entrez_Gene/asn_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Cache_Entrez_Gene/egene_ini":{"sourceIDs":["passdata"]}}},"ab_initio_antifam":{"label":"Bacterial Annotation, ab initio (first pass) searched against AntiFam","run":"bacterial_annot/wf_ab_initio_antifam.cwl","runType":"WORKFLOW","sources":{"ab_initio_antifam":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_antifam/models1":{"sourceIDs":["ab_initio_training"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_antifam/AntiFamLib":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_antifam/sequence_cache":{"sourceIDs":["genomic_source"]}}},"protein_alignment":{"label":"Align reference proteins plane complete workflow, with miniprot","run":"protein_alignment/wf_protein_alignment_miniprot.cwl","runType":"WORKFLOW","sources":{"protein_alignment":{"sourceIDs":["Get_Proteins"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/blastdb_dir":{"sourceIDs":["Create_Genomic_BLASTdb"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/genomic_ids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/compartments":{"sourceIDs":["bacterial_annot_1st_pass"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#protein_alignment/uniColl_asn_cache":{"sourceIDs":["passdata"]}}},"ab_initio_training":{"label":"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)","run":"bacterial_annot/wf_ab_initio_training.cwl","runType":"WORKFLOW","sources":{"ab_initio_training":{"sourceIDs":["bacterial_noncoding"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/inseq":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/trna_annots":{"sourceIDs":["bacterial_trna"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/ncrna_annots":{"sourceIDs":["bacterial_ncrna"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/selenoproteins":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/Execute_CRISPRs_annots":{"sourceIDs":["bacterial_mobile_elem"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/Generate_16S_rRNA_Annotation_annotation":{"sourceIDs":["bacterial_noncoding"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#ab_initio_training/Post_process_CMsearch_annotations_annots_5S":{"sourceIDs":["bacterial_noncoding"]}}},"add_checksum_gbent":{"run":"progs/annot_checksum.cwl","runType":"COMMANDLINETOOL","sources":{"add_checksum_gbent":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"bacterial_noncoding":{"label":"Non-Coding Bacterial Genes","run":"bacterial_noncoding/wf_bacterial_noncoding.cwl","runType":"WORKFLOW","sources":{"bacterial_noncoding":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/model_path_5s":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/model_path_16s":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/model_path_23s":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/rfam_stockholm":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_noncoding/rfam_amendments":{"sourceIDs":["passdata"]}}},"genus_list_file2ints":{"run":"progs/file2ints.cwl","runType":"EXPRESSIONTOOL","sources":{"genus_list_file2ints":{"sourceIDs":["blast_hits_cache_data_split_dir"]}}},"log_package_versions":{"doc":"concatenates input File[] to screen","run":"progs/catlog.cwl","runType":"COMMANDLINETOOL","sources":{"log_package_versions":{"sourceIDs":["passdata"]}}},"spurious_annot_final":{"label":"spurious_annot pass2","run":"spurious_annot/wf_spurious_annot_pass2.cwl","runType":"WORKFLOW","sources":{"spurious_annot_final":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/AntiFamLib":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/input_models":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/Extract_Model_Proteins_lds2":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_final/Extract_Model_Proteins_proteins":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]}}},"bacterial_mobile_elem":{"label":"Execute CRISPR","run":"bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl","runType":"WORKFLOW","sources":{"bacterial_mobile_elem":{"sourceIDs":["Prepare_Unannotated_Sequences_asnvalidate_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_mobile_elem/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_mobile_elem/seqids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_mobile_elem/asn_cache":{"sourceIDs":["genomic_source"]}}},"spurious_annot_prelim":{"label":"spurious_annot","run":"spurious_annot/wf_spurious_annot_pass1.cwl","runType":"WORKFLOW","sources":{"spurious_annot_prelim":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_prelim/AntiFamLib":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_prelim/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_prelim/Extract_ORF_Proteins_lds2":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_prelim/Extract_ORF_Proteins_seqids":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#spurious_annot_prelim/Extract_ORF_Proteins_proteins":{"sourceIDs":["orfs_hmms"]}}},"Create_Genomic_BLASTdb":{"label":"gp_makeblastdb","run":"progs/gp_makeblastdb.cwl","runType":"WORKFLOW","sources":{"Create_Genomic_BLASTdb":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Create_Genomic_BLASTdb/asn_cache":{"sourceIDs":["genomic_source"]}}},"bacterial_annot_1st_pass":{"label":"Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)","run":"bacterial_annot/wf_bacterial_annot_pass2.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_1st_pass":{"sourceIDs":["Get_Proteins"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/lds2":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/plasmids":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/proteins":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/raw_seqs":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/annotation":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/genus_list":{"sourceIDs":["genus_list_file2ints"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/prot_ids_A":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/prot_ids_B1":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/prot_ids_B2":{"sourceIDs":["spurious_annot_prelim"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/unicoll_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/blast_hits_cache":{"sourceIDs":["blast_hits_cache_data_split_dir"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/identification_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_1st_pass/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"Get_Order_Specific_Strings":{"run":"progs/file2basenames.cwl","runType":"EXPRESSIONTOOL","sources":{"Get_Order_Specific_Strings":{"sourceIDs":["passdata"]}}},"Prepare_Unannotated_Sequences":{"label":"Prepare Unannotated Sequences","doc":"Prepare Unannotated Sequences","run":"bacterial_prepare_unannotated.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences/ids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences/no_internet":{"sourceIDs":["no_internet"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences/submit_block":{"sourceIDs":["genomic_source"]}}},"Final_Bacterial_Package_ent2sqn":{"label":"ent2sqn","run":"progs/ent2sqn.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_ent2sqn":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_ent2sqn/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_ent2sqn/annotation":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_ent2sqn/gc_assembly":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_ent2sqn/contact_as_author_possible":{"sourceIDs":["contact_as_author_possible"]}}},"Generate_Annotation_Reports_gaf":{"label":"asn2flat","run":"progs/asn2gaf.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_gaf":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Generate_Annotation_Reports_gaf/input":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Generate_Annotation_Reports_gaf/go_hierarchy":{"sourceIDs":["passdata"]}}},"Generate_Annotation_Reports_gbk":{"label":"asn2flat","run":"progs/asn2flat.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_gbk":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"Generate_Annotation_Reports_gff":{"label":"gp_annot_format","run":"progs/gp_annot_format.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_gff":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]}}},"bacterial_annot_2nd_pass_blastp":{"label":"Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)","run":"bacterial_annot/wf_bacterial_annot_pass4.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_2nd_pass_blastp":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/lds2":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/blastdb":{"sourceIDs":["Get_Proteins"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/CDDdata2":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/proteins":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/annotation":{"sourceIDs":["spurious_annot_final"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/genus_list":{"sourceIDs":["genus_list_file2ints"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/wp_assignments":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/hmm_assignments":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/blast_hits_cache":{"sourceIDs":["blast_hits_cache_data_split_dir"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/defline_cleanup_rules":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/identification_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/Extract_Model_Proteins_prot_ids":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_blastp/Good_AntiFam_filtered_proteins_gilist":{"sourceIDs":["spurious_annot_final"]}}},"bacterial_orthology_conditional":{"label":"bacterial_orthology_cond","run":"bacterial_orthology/wf_bacterial_orthology_conditional.cwl","runType":"WORKFLOW","sources":{"bacterial_orthology_conditional":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/input":{"sourceIDs":["Add_Locus_Tags"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/gc_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/asn_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/genus_list":{"sourceIDs":["genus_list_file2ints"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/gencoll_asn":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_orthology_conditional/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"blast_hits_cache_data_split_dir":{"label":"Split input directory into subpath flows","run":"expr/blast_hits_cache_data_split_dir.cwl","runType":"EXPRESSIONTOOL","sources":{"blast_hits_cache_data_split_dir":{"sourceIDs":["blast_hits_cache_data"]}}},"Final_Bacterial_Package_sqn2gbent":{"label":"sqn2gbent","run":"progs/sqn2gbent.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_sqn2gbent":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]}}},"Final_Bacterial_Package_val_stats":{"label":"val_stats","run":"progs/val_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_val_stats":{"sourceIDs":["Final_Bacterial_Package_std_validation"]}}},"bacterial_annot_2nd_pass_genemark":{"label":"Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)","run":"bacterial_annot/wf_bacterial_annot_2nd_pass.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_2nd_pass_genemark":{"sourceIDs":["ab_initio_training"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/hmms_tab":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/raw_seqs":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/wp_hashes":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/annotation":{"sourceIDs":["ab_initio_training"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/hmm_aligns":{"sourceIDs":["orfs_hmms"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/prot_aligns":{"sourceIDs":["protein_alignment"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/selenoproteins":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/naming_hmms_combined":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#bacterial_annot_2nd_pass_genemark/good_ab_initio_annotations":{"sourceIDs":["ab_initio_antifam"]}}},"Prepare_Unannotated_Sequences_text":{"label":"asn_translator","run":"progs/asn_translator.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_text":{"sourceIDs":["Prepare_Unannotated_Sequences"]}}},"Final_Bacterial_Package_asn_cleanup":{"label":"asn_cleanup","run":"progs/asn_cleanup.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_asn_cleanup":{"sourceIDs":["bacterial_orthology_conditional"]}}},"Validate_Annotation_proc_annot_stats":{"label":"proc_annot_stats","run":"progs/proc_annot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_proc_annot_stats":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_proc_annot_stats/input":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_proc_annot_stats/univ_prot_xml":{"sourceIDs":["passdata"]}}},"Validate_Annotation_xsltproc_asndisc":{"label":"xsltproc","run":"progs/xsltproc.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_xsltproc_asndisc":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_xsltproc_asndisc/xml":{"sourceIDs":["Final_Bacterial_Package_std_validation"]}}},"Generate_Annotation_Reports_nuc_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_nuc_fasta":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"Final_Bacterial_Package_final_bact_asn":{"label":"final_bact_asn","run":"progs/final_bact_asn.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_final_bact_asn":{"sourceIDs":["Final_Bacterial_Package_asn_cleanup"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/order":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/gc_assembly":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/master_desc":{"sourceIDs":["Prepare_Unannotated_Sequences"]}}},"Final_Bacterial_Package_std_validation":{"label":"std_validation","run":"progs/std_validation.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_std_validation":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/ingb":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/inent":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/annotation":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/master_desc":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_std_validation/submit_block_template":{"sourceIDs":["genomic_source"]}}},"Generate_Annotation_Reports_prot_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_prot_fasta":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"Validate_Annotation_collect_annot_stats":{"label":"collect_annot_stats","run":"progs/collect_annot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_collect_annot_stats":{"sourceIDs":["Validate_Annotation_bact_univ_prot_stats"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_collect_annot_stats/input":{"sourceIDs":["Validate_Annotation_xsltproc_asnvalidate"]}}},"Final_Bacterial_Package_asndisc_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_asndisc_evaluate":{"sourceIDs":["xpath_fail_final_asndisc"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_asndisc_evaluate/input":{"sourceIDs":["Final_Bacterial_Package_std_validation"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_asndisc_evaluate/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]}}},"Validate_Annotation_bact_univ_prot_stats":{"label":"bact_univ_prot_stats","run":"progs/bact_univ_prot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_bact_univ_prot_stats":{"sourceIDs":["Final_Bacterial_Package_final_bact_asn"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/hmm_search":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/univ_prot_xml":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/val_res_den_xml":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/hmm_search_proteins":{"sourceIDs":["bacterial_annot_2nd_pass_genemark"]}}},"Validate_Annotation_xsltproc_asnvalidate":{"label":"xsltproc","run":"progs/xsltproc.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_xsltproc_asnvalidate":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_xsltproc_asnvalidate/xml":{"sourceIDs":["Final_Bacterial_Package_val_stats"]}}},"Generate_Annotation_Reports_cds_nuc_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_cds_nuc_fasta":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"Prepare_Unannotated_Sequences_asndisc_cpp":{"label":"asndisc_cpp","run":"progs/asndisc_cpp.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asndisc_cpp":{"sourceIDs":["Prepare_Unannotated_Sequences_text"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/asn_cache":{"sourceIDs":["genomic_source"]}}},"Prepare_Unannotated_Sequences_asnvalidate":{"label":"asnvalidate","run":"progs/asnvalidate.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asnvalidate":{"sourceIDs":["Prepare_Unannotated_Sequences"]}}},"Validate_Annotation_collect_annot_details":{"label":"collect_annot_stats","run":"progs/collect_annot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_collect_annot_details":{"sourceIDs":["Validate_Annotation_bact_univ_prot_stats"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Validate_Annotation_collect_annot_details/input":{"sourceIDs":["Validate_Annotation_proc_annot_stats"]}}},"Generate_Annotation_Reports_cds_prot_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_cds_prot_fasta":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]}}},"Final_Bacterial_Package_asnvalidate_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_asnvalidate_evaluate":{"sourceIDs":["xpath_fail_final_asnvalidate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_asnvalidate_evaluate/input":{"sourceIDs":["Final_Bacterial_Package_std_validation"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_asnvalidate_evaluate/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]}}},"Final_Bacterial_Package_dumb_down_as_required":{"label":"dumb_down_as_required","run":"progs/dumb_down_as_required.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_dumb_down_as_required":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/annotation":{"sourceIDs":["Final_Bacterial_Package_final_bact_asn"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/submol_block_json":{"sourceIDs":["submol_block_json"]}}},"Prepare_Unannotated_Sequences_asndisc_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asndisc_evaluate":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_cpp"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_evaluate/xpath_fail":{"sourceIDs":["xpath_fail_initial_asndisc"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_evaluate/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]}}},"Prepare_Unannotated_Sequences_pgapx_input_check":{"label":"pgapx_input_check","run":"progs/pgapx_input_check.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_pgapx_input_check":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/input":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/species_genome_size":{"sourceIDs":["passdata"]}}},"Prepare_Unannotated_Sequences_asnvalidate_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asnvalidate_evaluate":{"sourceIDs":["Prepare_Unannotated_Sequences_asnvalidate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate_evaluate/xpath_fail":{"sourceIDs":["xpath_fail_initial_asnvalidate"]},"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate_evaluate/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]}}}},"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    \"scatter_gather_nchunks\" [fillcolor=\"#94DDF4\",label=\"scatter_gather_nchunks\"];\n    \"xpath_fail_final_asndisc\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_final_asndisc\"];\n    \"contact_as_author_possible\" [fillcolor=\"#94DDF4\",label=\"contact_as_author_possible\"];\n    \"make_uuid\" [fillcolor=\"#94DDF4\",label=\"make_uuid\"];\n    \"taxid\" [fillcolor=\"#94DDF4\",label=\"taxid\"];\n    \"ignore_all_errors\" [fillcolor=\"#94DDF4\",label=\"ignore_all_errors\"];\n    \"locus_tag_prefix\" [fillcolor=\"#94DDF4\",label=\"locus_tag_prefix\"];\n    \"entries\" [fillcolor=\"#94DDF4\",label=\"entries\"];\n    \"submol_block_json\" [fillcolor=\"#94DDF4\",label=\"submol_block_json\"];\n    \"os_version\" [fillcolor=\"#94DDF4\",label=\"os_version\"];\n    \"report_usage\" [fillcolor=\"#94DDF4\",label=\"report_usage\"];\n    \"supplemental_data\" [fillcolor=\"#94DDF4\",label=\"supplemental_data\"];\n    \"gc_assm_name\" [fillcolor=\"#94DDF4\",label=\"gc_assm_name\"];\n    \"seq_submit\" [fillcolor=\"#94DDF4\",label=\"seq_submit\"];\n    \"blast_hits_cache_data\" [fillcolor=\"#94DDF4\",label=\"blast_hits_cache_data\"];\n    \"uuid_in\" [fillcolor=\"#94DDF4\",label=\"uuid_in\"];\n    \"xpath_fail_initial_asnvalidate\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_initial_asnvalidate\"];\n    \"go\" [fillcolor=\"#94DDF4\",label=\"go\"];\n    \"xpath_fail_final_asnvalidate\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_final_asnvalidate\"];\n    \"no_internet\" [fillcolor=\"#94DDF4\",label=\"no_internet\"];\n    \"dbname\" [fillcolor=\"#94DDF4\",label=\"dbname\"];\n    \"xpath_fail_initial_asndisc\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_initial_asndisc\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"checkm_raw\" [fillcolor=\"#94DDF4\",label=\"checkm_raw\"];\n    \"gff\" [fillcolor=\"#94DDF4\",label=\"gff\"];\n    \"nucleotide_fasta\" [fillcolor=\"#94DDF4\",label=\"nucleotide_fasta\"];\n    \"sqn\" [fillcolor=\"#94DDF4\",label=\"sqn\"];\n    \"protein_fasta\" [fillcolor=\"#94DDF4\",label=\"protein_fasta\"];\n    \"gbent\" [fillcolor=\"#94DDF4\",label=\"gbent\"];\n    \"proc_annot_stats\" [fillcolor=\"#94DDF4\",label=\"proc_annot_stats\"];\n    \"final_asnval_error_diag\" [fillcolor=\"#94DDF4\",label=\"final_asnval_error_diag\"];\n    \"gbk\" [fillcolor=\"#94DDF4\",label=\"gbk\"];\n    \"initial_asndisc_error_diag\" [fillcolor=\"#94DDF4\",label=\"initial_asndisc_error_diag\"];\n    \"cds_nucleotide_fasta\" [fillcolor=\"#94DDF4\",label=\"cds_nucleotide_fasta\"];\n    \"gaf\" [fillcolor=\"#94DDF4\",label=\"gaf\"];\n    \"cds_protein_fasta\" [fillcolor=\"#94DDF4\",label=\"cds_protein_fasta\"];\n    \"final_asndisc_error_diag\" [fillcolor=\"#94DDF4\",label=\"final_asndisc_error_diag\"];\n    \"checkm_results\" [fillcolor=\"#94DDF4\",label=\"checkm_results\"];\n    \"all_proc_annot_stats\" [fillcolor=\"#94DDF4\",label=\"all_proc_annot_stats\"];\n    \"initial_asnval_error_diag\" [fillcolor=\"#94DDF4\",label=\"initial_asnval_error_diag\"];\n  }\n  \"ping_stop\" [label=\"pinger\"];\n  \"spurious_annot_final\" [label=\"spurious_annot pass2\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"xml_evaluate\"];\n  \"Final_Bacterial_Package_final_bact_asn\" [label=\"final_bact_asn\"];\n  \"Validate_Annotation_bact_univ_prot_stats\" [label=\"bact_univ_prot_stats\"];\n  \"Validate_Annotation_xsltproc_asndisc\" [label=\"xsltproc\"];\n  \"Final_Bacterial_Package_sqn2gbent\" [label=\"sqn2gbent\"];\n  \"add_checksum_gbent\" [label=\"add_checksum_gbent\"];\n  \"Cache_Entrez_Gene\" [label=\"Cache Entrez Gene\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"dumb_down_as_required\"];\n  \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"asndisc_cpp\"];\n  \"Generate_Annotation_Reports_gaf\" [label=\"asn2flat\"];\n  \"Add_Locus_Tags\" [label=\"add_locus_tags\"];\n  \"Final_Bacterial_Package_asn_cleanup\" [label=\"asn_cleanup\"];\n  \"Validate_Annotation_proc_annot_stats\" [label=\"proc_annot_stats\"];\n  \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"pgapx_input_check\"];\n  \"passdata\" [label=\"Split input directory into subpath flows\"];\n  \"ab_initio_antifam\" [label=\"Bacterial Annotation, ab initio (first pass) searched against AntiFam\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_gbk\" [label=\"asn2flat\"];\n  \"ping_start\" [label=\"pinger\"];\n  \"ab_initio_training\" [label=\"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"xml_evaluate\"];\n  \"bacterial_noncoding\" [label=\"Non-Coding Bacterial Genes\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_ent2sqn\" [label=\"ent2sqn\"];\n  \"add_checksum_sqn\" [label=\"add_checksum_sqn\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"asnvalidate\"];\n  \"Validate_Annotation_collect_annot_details\" [label=\"collect_annot_stats\"];\n  \"bacterial_annot_2nd_pass_blastp\" [label=\"Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_cds_prot_fasta\" [label=\"asn2fasta\"];\n  \"log_package_versions\" [label=\"log_package_versions\"];\n  \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"xml_evaluate\"];\n  \"Generate_Annotation_Reports_gff\" [label=\"gp_annot_format\"];\n  \"bacterial_mobile_elem\" [label=\"Execute CRISPR\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences\" [label=\"Prepare Unannotated Sequences\"];\n  \"Get_Order_Specific_Strings\" [label=\"Get_Order_Specific_Strings\"];\n  \"checkm\" [label=\"checkm\", fillcolor=\"#F3CEA1\"];\n  \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xsltproc\"];\n  \"genus_list_file2ints\" [label=\"genus_list_file2ints\"];\n  \"Final_Bacterial_Package_std_validation\" [label=\"std_validation\"];\n  \"bacterial_annot_2nd_pass_genemark\" [label=\"Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_cds_nuc_fasta\" [label=\"asn2fasta\"];\n  \"genomic_source\" [label=\"Create Genomic Collection for Bacterial Pipeline, ASN.1 input\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_text\" [label=\"asn_translator\"];\n  \"protein_alignment\" [label=\"Align reference proteins plane complete workflow, with miniprot\", fillcolor=\"#F3CEA1\"];\n  \"bacterial_annot_1st_pass\" [label=\"Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)\", fillcolor=\"#F3CEA1\"];\n  \"Get_Proteins\" [label=\"Get Proteins\", fillcolor=\"#F3CEA1\"];\n  \"spurious_annot_prelim\" [label=\"spurious_annot\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_nuc_fasta\" [label=\"asn2fasta\"];\n  \"Validate_Annotation_collect_annot_stats\" [label=\"collect_annot_stats\"];\n  \"bacterial_orthology_conditional\" [label=\"bacterial_orthology_cond\", fillcolor=\"#F3CEA1\"];\n  \"Create_Genomic_BLASTdb\" [label=\"gp_makeblastdb\", fillcolor=\"#F3CEA1\"];\n  \"bacterial_ncrna\" [label=\"Run genomic CMsearch (Rfam rRNA)\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_prot_fasta\" [label=\"asn2fasta\"];\n  \"blast_hits_cache_data_split_dir\" [label=\"Split input directory into subpath flows\"];\n  \"bacterial_trna\" [label=\"Run tRNAScan\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"xml_evaluate\"];\n  \"Final_Bacterial_Package_val_stats\" [label=\"val_stats\"];\n  \"orfs_hmms\" [label=\"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)\", fillcolor=\"#F3CEA1\"];\n  \"ping_start\" -> \"ping_stop\" [label=\"uuid_in\"];\n  \"report_usage\" -> \"ping_stop\" [label=\"report_usage\"];\n  \"os_version\" -> \"ping_stop\" [label=\"os_version\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"ping_stop\" [label=\"infile\"];\n  \"Generate_Annotation_Reports_gff\" -> \"ping_stop\" [label=\"infile\"];\n  \"Generate_Annotation_Reports_nuc_fasta\" -> \"ping_stop\" [label=\"infile\"];\n  \"Generate_Annotation_Reports_prot_fasta\" -> \"ping_stop\" [label=\"infile\"];\n  \"Generate_Annotation_Reports_gbk\" -> \"ping_stop\" [label=\"infile\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"spurious_annot_final\" [label=\"Extract_Model_Proteins_seqids\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"spurious_annot_final\" [label=\"Extract_Model_Proteins_proteins\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"spurious_annot_final\" [label=\"Extract_Model_Proteins_lds2\"];\n  \"genomic_source\" -> \"spurious_annot_final\" [label=\"sequence_cache\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"spurious_annot_final\" [label=\"input_models\"];\n  \"scatter_gather_nchunks\" -> \"spurious_annot_final\" [label=\"scatter_gather_nchunks\"];\n  \"passdata\" -> \"spurious_annot_final\" [label=\"AntiFamLib\"];\n  \"xpath_fail_final_asnvalidate\" -> \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"xpath_fail\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"input\"];\n  \"ignore_all_errors\" -> \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"ignore_all_errors\"];\n  \"Final_Bacterial_Package_asn_cleanup\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"annotation\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"asn_cache\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"gc_assembly\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"master_desc\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"order\"];\n  \"Final_Bacterial_Package_final_bact_asn\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"input\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"hmm_search_proteins\"];\n  \"passdata\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"univ_prot_xml\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"hmm_search\"];\n  \"passdata\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"val_res_den_xml\"];\n  \"passdata\" -> \"Validate_Annotation_xsltproc_asndisc\" [label=\"xslt\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Validate_Annotation_xsltproc_asndisc\" [label=\"xml\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"Final_Bacterial_Package_sqn2gbent\" [label=\"input\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"add_checksum_gbent\" [label=\"input\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Cache_Entrez_Gene\" [label=\"input\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"Cache_Entrez_Gene\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"Cache_Entrez_Gene\" [label=\"go\"];\n  \"passdata\" -> \"Cache_Entrez_Gene\" [label=\"egene_ini\"];\n  \"genomic_source\" -> \"Cache_Entrez_Gene\" [label=\"asn_cache\"];\n  \"passdata\" -> \"Cache_Entrez_Gene\" [label=\"asn_cache\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"asn_cache\"];\n  \"submol_block_json\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"submol_block_json\"];\n  \"Final_Bacterial_Package_final_bact_asn\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"annotation\"];\n  \"Prepare_Unannotated_Sequences_text\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"i\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"asn_cache\"];\n  \"taxid\" -> \"Generate_Annotation_Reports_gaf\" [label=\"taxid\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_gaf\" [label=\"input\"];\n  \"passdata\" -> \"Generate_Annotation_Reports_gaf\" [label=\"go_hierarchy\"];\n  \"locus_tag_prefix\" -> \"Add_Locus_Tags\" [label=\"locus_tag_prefix\"];\n  \"bacterial_annot_2nd_pass_blastp\" -> \"Add_Locus_Tags\" [label=\"input\"];\n  \"dbname\" -> \"Add_Locus_Tags\" [label=\"dbname\"];\n  \"bacterial_orthology_conditional\" -> \"Final_Bacterial_Package_asn_cleanup\" [label=\"inp_annotation\"];\n  \"passdata\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"val_res_den_xml\"];\n  \"passdata\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"univ_prot_xml\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"input\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"taxon_db\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"species_genome_size\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"input\"];\n  \"ignore_all_errors\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"ignore_all_errors\"];\n  \"supplemental_data\" -> \"passdata\" [label=\"data\"];\n  \"scatter_gather_nchunks\" -> \"ab_initio_antifam\" [label=\"scatter_gather_nchunks\"];\n  \"genomic_source\" -> \"ab_initio_antifam\" [label=\"sequence_cache\"];\n  \"ab_initio_training\" -> \"ab_initio_antifam\" [label=\"models1\"];\n  \"passdata\" -> \"ab_initio_antifam\" [label=\"AntiFamLib\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_gbk\" [label=\"input\"];\n  \"make_uuid\" -> \"ping_start\" [label=\"make_uuid\"];\n  \"os_version\" -> \"ping_start\" [label=\"os_version\"];\n  \"uuid_in\" -> \"ping_start\" [label=\"uuid_in\"];\n  \"gc_assm_name\" -> \"ping_start\" [label=\"instring\"];\n  \"report_usage\" -> \"ping_start\" [label=\"report_usage\"];\n  \"bacterial_noncoding\" -> \"ab_initio_training\" [label=\"Generate_23S_rRNA_Annotation_annotation\"];\n  \"passdata\" -> \"ab_initio_training\" [label=\"selenoproteins\"];\n  \"bacterial_noncoding\" -> \"ab_initio_training\" [label=\"Generate_16S_rRNA_Annotation_annotation\"];\n  \"passdata\" -> \"ab_initio_training\" [label=\"uniColl_cache\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"ab_initio_training\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"ab_initio_training\" [label=\"go\"];\n  \"bacterial_trna\" -> \"ab_initio_training\" [label=\"trna_annots\"];\n  \"bacterial_mobile_elem\" -> \"ab_initio_training\" [label=\"Execute_CRISPRs_annots\"];\n  \"Prepare_Unannotated_Sequences\" -> \"ab_initio_training\" [label=\"inseq\"];\n  \"passdata\" -> \"ab_initio_training\" [label=\"naming_sqlite\"];\n  \"bacterial_noncoding\" -> \"ab_initio_training\" [label=\"Post_process_CMsearch_annotations_annots_5S\"];\n  \"genomic_source\" -> \"ab_initio_training\" [label=\"asn_cache\"];\n  \"bacterial_ncrna\" -> \"ab_initio_training\" [label=\"ncrna_annots\"];\n  \"passdata\" -> \"ab_initio_training\" [label=\"thresholds\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"input\"];\n  \"xpath_fail_initial_asnvalidate\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"xpath_fail\"];\n  \"ignore_all_errors\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"ignore_all_errors\"];\n  \"genomic_source\" -> \"bacterial_noncoding\" [label=\"seqids\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"model_path_5s\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"taxon_db\"];\n  \"genomic_source\" -> \"bacterial_noncoding\" [label=\"asn_cache\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"model_path_16s\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"rfam_amendments\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"rfam_stockholm\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"model_path_23s\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_noncoding\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_noncoding\" [label=\"go\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"submit_block_template\"];\n  \"contact_as_author_possible\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"contact_as_author_possible\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"annotation\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"gc_assembly\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"asn_cache\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"add_checksum_sqn\" [label=\"input\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"i\"];\n  \"Validate_Annotation_bact_univ_prot_stats\" -> \"Validate_Annotation_collect_annot_details\" [label=\"input\"];\n  \"Validate_Annotation_proc_annot_stats\" -> \"Validate_Annotation_collect_annot_details\" [label=\"input\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"CDDdata\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"proteins\"];\n  \"genus_list_file2ints\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"genus_list\"];\n  \"Get_Proteins\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"blastdb\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"naming_sqlite\"];\n  \"spurious_annot_final\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"annotation\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"hmm_assignments\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"Extract_Model_Proteins_prot_ids\"];\n  \"genomic_source\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"sequence_cache\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"defline_cleanup_rules\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"wp_assignments\"];\n  \"blast_hits_cache_data_split_dir\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"blast_hits_cache\"];\n  \"spurious_annot_final\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"Good_AntiFam_filtered_proteins_gilist\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"identification_db_dir\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"thresholds\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"CDDdata2\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"scatter_gather_nchunks\"];\n  \"taxid\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"taxid\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"uniColl_cache\"];\n  \"bacterial_annot_2nd_pass_genemark\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"lds2\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_blastp\" [label=\"taxon_db\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_cds_prot_fasta\" [label=\"i\"];\n  \"passdata\" -> \"log_package_versions\" [label=\"input\"];\n  \"xpath_fail_final_asndisc\" -> \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"xpath_fail\"];\n  \"ignore_all_errors\" -> \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"ignore_all_errors\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"input\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Generate_Annotation_Reports_gff\" [label=\"input\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_mobile_elem\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_mobile_elem\" [label=\"go\"];\n  \"genomic_source\" -> \"bacterial_mobile_elem\" [label=\"asn_cache\"];\n  \"genomic_source\" -> \"bacterial_mobile_elem\" [label=\"seqids\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"gc_assembly\"];\n  \"no_internet\" -> \"Prepare_Unannotated_Sequences\" [label=\"no_internet\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"asn_cache\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences\" [label=\"taxon_db\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"submit_block\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"ids\"];\n  \"passdata\" -> \"Get_Order_Specific_Strings\" [label=\"input\"];\n  \"taxid\" -> \"checkm\" [label=\"taxid\"];\n  \"passdata\" -> \"checkm\" [label=\"taxon_db\"];\n  \"passdata\" -> \"checkm\" [label=\"filter_for_raw_checkm\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"checkm\" [label=\"models\"];\n  \"passdata\" -> \"checkm\" [label=\"checkm_data_path\"];\n  \"passdata\" -> \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xslt\"];\n  \"Final_Bacterial_Package_val_stats\" -> \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xml\"];\n  \"blast_hits_cache_data_split_dir\" -> \"genus_list_file2ints\" [label=\"input\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"Final_Bacterial_Package_std_validation\" [label=\"insqn\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Final_Bacterial_Package_std_validation\" [label=\"ingb\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_std_validation\" [label=\"submit_block_template\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Final_Bacterial_Package_std_validation\" [label=\"master_desc\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_std_validation\" [label=\"asn_cache\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Final_Bacterial_Package_std_validation\" [label=\"annotation\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Final_Bacterial_Package_std_validation\" [label=\"inent\"];\n  \"ab_initio_training\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"hmm_params\"];\n  \"ab_initio_antifam\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"good_ab_initio_annotations\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"taxon_db\"];\n  \"genomic_source\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"sequence_cache\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"scatter_gather_nchunks\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"hmms_tab\"];\n  \"protein_alignment\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"prot_aligns\"];\n  \"orfs_hmms\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"hmm_aligns\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"selenoproteins\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"thresholds\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"uniColl_cache\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"wp_hashes\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"naming_hmms_combined\"];\n  \"ab_initio_training\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"annotation\"];\n  \"Prepare_Unannotated_Sequences\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"raw_seqs\"];\n  \"passdata\" -> \"bacterial_annot_2nd_pass_genemark\" [label=\"naming_sqlite\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_cds_nuc_fasta\" [label=\"i\"];\n  \"passdata\" -> \"genomic_source\" [label=\"taxon_db\"];\n  \"entries\" -> \"genomic_source\" [label=\"entries\"];\n  \"seq_submit\" -> \"genomic_source\" [label=\"seq_submit\"];\n  \"ping_start\" -> \"genomic_source\" [label=\"gc_assm_name\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_text\" [label=\"input\"];\n  \"Get_Proteins\" -> \"protein_alignment\" [label=\"all_prots\"];\n  \"Create_Genomic_BLASTdb\" -> \"protein_alignment\" [label=\"blastdb_dir\"];\n  \"bacterial_annot_1st_pass\" -> \"protein_alignment\" [label=\"compartments\"];\n  \"passdata\" -> \"protein_alignment\" [label=\"taxon_db\"];\n  \"passdata\" -> \"protein_alignment\" [label=\"uniColl_asn_cache\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"protein_alignment\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"protein_alignment\" [label=\"go\"];\n  \"genomic_source\" -> \"protein_alignment\" [label=\"asn_cache\"];\n  \"taxid\" -> \"protein_alignment\" [label=\"taxid\"];\n  \"genomic_source\" -> \"protein_alignment\" [label=\"genomic_ids\"];\n  \"Get_Proteins\" -> \"bacterial_annot_1st_pass\" [label=\"blastdb\"];\n  \"orfs_hmms\" -> \"bacterial_annot_1st_pass\" [label=\"annotation\"];\n  \"orfs_hmms\" -> \"bacterial_annot_1st_pass\" [label=\"lds2\"];\n  \"passdata\" -> \"bacterial_annot_1st_pass\" [label=\"identification_db_dir\"];\n  \"orfs_hmms\" -> \"bacterial_annot_1st_pass\" [label=\"prot_ids_B1\"];\n  \"passdata\" -> \"bacterial_annot_1st_pass\" [label=\"taxon_db\"];\n  \"orfs_hmms\" -> \"bacterial_annot_1st_pass\" [label=\"prot_ids_A\"];\n  \"orfs_hmms\" -> \"bacterial_annot_1st_pass\" [label=\"proteins\"];\n  \"spurious_annot_prelim\" -> \"bacterial_annot_1st_pass\" [label=\"prot_ids_B2\"];\n  \"passdata\" -> \"bacterial_annot_1st_pass\" [label=\"unicoll_cache\"];\n  \"Prepare_Unannotated_Sequences\" -> \"bacterial_annot_1st_pass\" [label=\"plasmids\"];\n  \"genomic_source\" -> \"bacterial_annot_1st_pass\" [label=\"sequence_cache\"];\n  \"genus_list_file2ints\" -> \"bacterial_annot_1st_pass\" [label=\"genus_list\"];\n  \"Prepare_Unannotated_Sequences\" -> \"bacterial_annot_1st_pass\" [label=\"raw_seqs\"];\n  \"blast_hits_cache_data_split_dir\" -> \"bacterial_annot_1st_pass\" [label=\"blast_hits_cache\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_1st_pass\" [label=\"scatter_gather_nchunks\"];\n  \"taxid\" -> \"bacterial_annot_1st_pass\" [label=\"taxid\"];\n  \"taxid\" -> \"Get_Proteins\" [label=\"taxid\"];\n  \"passdata\" -> \"Get_Proteins\" [label=\"uniColl_asn_cache\"];\n  \"Get_Order_Specific_Strings\" -> \"Get_Proteins\" [label=\"all_order_specific_blastdb\"];\n  \"passdata\" -> \"Get_Proteins\" [label=\"blastdb_dir\"];\n  \"passdata\" -> \"Get_Proteins\" [label=\"naming_sqlite\"];\n  \"passdata\" -> \"Get_Proteins\" [label=\"tax_sql_file\"];\n  \"genomic_source\" -> \"spurious_annot_prelim\" [label=\"sequence_cache\"];\n  \"orfs_hmms\" -> \"spurious_annot_prelim\" [label=\"Extract_ORF_Proteins_seqids\"];\n  \"passdata\" -> \"spurious_annot_prelim\" [label=\"AntiFamLib\"];\n  \"orfs_hmms\" -> \"spurious_annot_prelim\" [label=\"Extract_ORF_Proteins_lds2\"];\n  \"scatter_gather_nchunks\" -> \"spurious_annot_prelim\" [label=\"scatter_gather_nchunks\"];\n  \"orfs_hmms\" -> \"spurious_annot_prelim\" [label=\"Extract_ORF_Proteins_proteins\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_nuc_fasta\" [label=\"i\"];\n  \"Validate_Annotation_bact_univ_prot_stats\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"input\"];\n  \"Validate_Annotation_xsltproc_asndisc\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"input\"];\n  \"Validate_Annotation_proc_annot_stats\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"input\"];\n  \"Validate_Annotation_xsltproc_asnvalidate\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"input\"];\n  \"genomic_source\" -> \"bacterial_orthology_conditional\" [label=\"asn_cache\"];\n  \"passdata\" -> \"bacterial_orthology_conditional\" [label=\"asn_cache\"];\n  \"Add_Locus_Tags\" -> \"bacterial_orthology_conditional\" [label=\"input\"];\n  \"genus_list_file2ints\" -> \"bacterial_orthology_conditional\" [label=\"genus_list\"];\n  \"genomic_source\" -> \"bacterial_orthology_conditional\" [label=\"gencoll_asn\"];\n  \"passdata\" -> \"bacterial_orthology_conditional\" [label=\"taxon_db\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_orthology_conditional\" [label=\"scatter_gather_nchunks\"];\n  \"passdata\" -> \"bacterial_orthology_conditional\" [label=\"naming_sqlite\"];\n  \"taxid\" -> \"bacterial_orthology_conditional\" [label=\"taxid\"];\n  \"passdata\" -> \"bacterial_orthology_conditional\" [label=\"gc_cache\"];\n  \"genomic_source\" -> \"Create_Genomic_BLASTdb\" [label=\"ids\"];\n  \"genomic_source\" -> \"Create_Genomic_BLASTdb\" [label=\"asn_cache\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_ncrna\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_ncrna\" [label=\"go\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"taxon_db\"];\n  \"genomic_source\" -> \"bacterial_ncrna\" [label=\"asn_cache\"];\n  \"genomic_source\" -> \"bacterial_ncrna\" [label=\"seqids\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"rfam_stockholm\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"rfam_amendments\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"model_path\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_prot_fasta\" [label=\"i\"];\n  \"blast_hits_cache_data\" -> \"blast_hits_cache_data_split_dir\" [label=\"data\"];\n  \"genomic_source\" -> \"bacterial_trna\" [label=\"seqids\"];\n  \"taxid\" -> \"bacterial_trna\" [label=\"taxid\"];\n  \"genomic_source\" -> \"bacterial_trna\" [label=\"asn_cache\"];\n  \"passdata\" -> \"bacterial_trna\" [label=\"taxon_db\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_trna\" [label=\"scatter_gather_nchunks\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_trna\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_trna\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_cpp\" -> \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"input\"];\n  \"xpath_fail_initial_asndisc\" -> \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"xpath_fail\"];\n  \"ignore_all_errors\" -> \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"ignore_all_errors\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Final_Bacterial_Package_val_stats\" [label=\"annot_val\"];\n  \"Prepare_Unannotated_Sequences\" -> \"orfs_hmms\" [label=\"inseq\"];\n  \"scatter_gather_nchunks\" -> \"orfs_hmms\" [label=\"scatter_gather_nchunks\"];\n  \"passdata\" -> \"orfs_hmms\" [label=\"hmm_path\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"orfs_hmms\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"orfs_hmms\" [label=\"go\"];\n  \"genomic_source\" -> \"orfs_hmms\" [label=\"asn_cache\"];\n  \"passdata\" -> \"orfs_hmms\" [label=\"uniColl_cache\"];\n  \"passdata\" -> \"orfs_hmms\" [label=\"hmms_tab\"];\n  \"ab_initio_antifam\" -> \"orfs_hmms\" [label=\"annotation\"];\n  \"checkm\" -> \"checkm_raw\";\n  \"Generate_Annotation_Reports_gff\" -> \"gff\";\n  \"Generate_Annotation_Reports_nuc_fasta\" -> \"nucleotide_fasta\";\n  \"add_checksum_sqn\" -> \"sqn\";\n  \"Generate_Annotation_Reports_prot_fasta\" -> \"protein_fasta\";\n  \"add_checksum_gbent\" -> \"gbent\";\n  \"Validate_Annotation_proc_annot_stats\" -> \"proc_annot_stats\";\n  \"Final_Bacterial_Package_asnvalidate_evaluate\" -> \"final_asnval_error_diag\";\n  \"Generate_Annotation_Reports_gbk\" -> \"gbk\";\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"initial_asndisc_error_diag\";\n  \"Generate_Annotation_Reports_cds_nuc_fasta\" -> \"cds_nucleotide_fasta\";\n  \"Generate_Annotation_Reports_gaf\" -> \"gaf\";\n  \"Generate_Annotation_Reports_cds_prot_fasta\" -> \"cds_protein_fasta\";\n  \"Final_Bacterial_Package_asndisc_evaluate\" -> \"final_asndisc_error_diag\";\n  \"checkm\" -> \"checkm_results\";\n  \"Validate_Annotation_collect_annot_stats\" -> \"all_proc_annot_stats\";\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"initial_asnval_error_diag\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/wf_common.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/LICENSE.md"}