{"@id":"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","retrievedFrom":{"repoUrl":"https://github.com/ncbi/pgap.git","branch":"4def84df33963fc9ac9d5c5f804b911d01a0d9ad","path":"wf_common.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","url":"https://github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl"},"retrievedOn":"2026-09-21T12:20:35.492+00:00","lastCommit":"4def84df33963fc9ac9d5c5f804b911d01a0d9ad","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)"},"seq_submit":{"type":"File (Optional)"},"no_internet":{"type":"Boolean (Optional)"},"gc_assm_name":{"type":"String"},"report_usage":{"type":"Boolean"},"blast_rules_db":{"type":"String"},"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":{"gbk":{"type":"File"},"gff":{"type":"File"},"sqn":{"type":"File"},"gbent":{"type":"File"},"protein_fasta":{"type":"File (Optional)"},"nucleotide_fasta":{"type":"File (Optional)"},"proc_annot_stats":{"type":"File"}},"steps":{"passdata":{"label":"Split input directory into subpath flows","run":"expr/supplemental_data_split_dir.cwl","runType":"EXPRESSIONTOOL","sources":{"passdata":{"sourceIDs":["supplemental_data"]}}},"ping_stop":{"label":"pinger","run":"progs/pinger.cwl","runType":"COMMANDLINETOOL","sources":{"ping_stop":{"defaultVal":"\\\"stop\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_stop/infile":{"sourceIDs":["Generate_Annotation_Reports_prot_fasta"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_stop/uuid_in":{"sourceIDs":["ping_start"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_stop/workflow":{"defaultVal":"\\\"pgap\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_stop/report_usage":{"sourceIDs":["report_usage"]}}},"ping_start":{"label":"pinger","run":"progs/pinger.cwl","runType":"COMMANDLINETOOL","sources":{"ping_start":{"defaultVal":"\\\"pgap\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_start/state":{"defaultVal":"\\\"start\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_start/instring":{"sourceIDs":["gc_assm_name"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_start/make_uuid":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#ping_start/report_usage":{"sourceIDs":["report_usage"]}}},"Add_Locus_Tags":{"label":"add_locus_tags","run":"progs/add_locus_tags.cwl","runType":"COMMANDLINETOOL","sources":{"Add_Locus_Tags":{"sourceIDs":["bacterial_annot_4"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Add_Locus_Tags/dbname":{"sourceIDs":["dbname"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Add_Locus_Tags/locus_tag_prefix":{"sourceIDs":["locus_tag_prefix"]}}},"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/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_trna/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_trna/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_trna/seqids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_trna/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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":["ping_start"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#genomic_source/entries":{"sourceIDs":["entries"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#genomic_source/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#genomic_source/seq_submit":{"sourceIDs":["seq_submit"]}}},"bacterial_annot":{"label":"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)","run":"bacterial_annot/wf_bacterial_annot_pass1.cwl","runType":"WORKFLOW","sources":{"bacterial_annot":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/hmm_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/hmms_tab":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/nogenbank":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/trna_annots":{"sourceIDs":["bacterial_trna"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/ncrna_annots":{"sourceIDs":["bacterial_ncrna"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/genemark_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/selenoproteins":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/Execute_CRISPRs_annots":{"sourceIDs":["bacterial_mobile_elem"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/Generate_16S_rRNA_Annotation_annotation":{"sourceIDs":["bacterial_noncoding"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/Generate_23S_rRNA_Annotation_annotation":{"sourceIDs":["bacterial_noncoding"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot/Post_process_CMsearch_annotations_annots_5S":{"sourceIDs":["bacterial_noncoding"]}}},"bacterial_ncrna":{"label":"Run genomic CMsearch (Rfam rRNA)","run":"bacterial_ncrna/wf_gcmsearch.cwl","runType":"WORKFLOW","sources":{"bacterial_ncrna":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/seqids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/rfam_stockholm":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_ncrna/rfam_amendments":{"sourceIDs":["passdata"]}}},"add_checksum_sqn":{"run":"progs/annot_checksum.cwl","runType":"COMMANDLINETOOL","sources":{"add_checksum_sqn":{"defaultVal":"\\\"annot.sqn\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_sqn/t":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_sqn/ifmt":{"defaultVal":"\\\"seq-submit\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_sqn/mode":{"defaultVal":"\\\"add\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_sqn/input":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]}}},"spurious_annot_1":{"label":"spurious_annot","run":"spurious_annot/wf_spurious_annot_pass1.cwl","runType":"WORKFLOW","sources":{"spurious_annot_1":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_1/AntiFamLib":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_1/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_1/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_1/Extract_ORF_Proteins_lds2":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_1/Extract_ORF_Proteins_proteins":{"sourceIDs":["bacterial_annot"]}}},"spurious_annot_2":{"label":"spurious_annot pass2","run":"spurious_annot/wf_spurious_annot_pass2.cwl","runType":"WORKFLOW","sources":{"spurious_annot_2":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/Run_GeneMark_models":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/Extract_Model_Proteins_lds2":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/Extract_Model_Proteins_seqids":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#spurious_annot_2/Extract_Model_Proteins_proteins":{"sourceIDs":["bacterial_annot_3"]}}},"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/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Cache_Entrez_Gene/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Cache_Entrez_Gene/asn_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Cache_Entrez_Gene/egene_ini":{"sourceIDs":["passdata"]}}},"bacterial_annot_2":{"label":"Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)","run":"bacterial_annot/wf_bacterial_annot_pass2.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_2":{"sourceIDs":["genus_list_file2ints"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/lds2":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/proteins":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/annotation":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/prot_ids_A":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/prot_ids_B1":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/prot_ids_B2":{"sourceIDs":["spurious_annot_1"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/unicoll_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/blast_rules_db":{"sourceIDs":["blast_rules_db"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/blast_hits_cache":{"sourceIDs":["blast_hits_cache_data_split_dir"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/blast_rules_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/identification_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_2/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"bacterial_annot_3":{"label":"Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)","run":"bacterial_annot/wf_bacterial_annot_pass3.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_3":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/models1":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/hmms_tab":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/raw_seqs":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/wp_hashes":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/annotation":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/hmm_aligns":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/hmm_params":{"sourceIDs":["bacterial_annot"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/prot_aligns":{"sourceIDs":["protein_alignment"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/genemark_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/uniColl_cache":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/naming_hmms_combined":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_3/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]}}},"bacterial_annot_4":{"label":"Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)","run":"bacterial_annot/wf_bacterial_annot_pass4.cwl","runType":"WORKFLOW","sources":{"bacterial_annot_4":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/lds2":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/CDDdata":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/CDDdata2":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/proteins":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/annotation":{"sourceIDs":["spurious_annot_2"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/genus_list":{"sourceIDs":["genus_list_file2ints"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/thresholds":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/naming_sqlite":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/blast_rules_db":{"sourceIDs":["blast_rules_db"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/sequence_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/wp_assignments":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/hmm_assignments":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/naming_blast_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/blast_hits_cache":{"sourceIDs":["blast_hits_cache_data_split_dir"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/blast_rules_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/defline_cleanup_rules":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/identification_db_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/scatter_gather_nchunks":{"sourceIDs":["scatter_gather_nchunks"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/Extract_Model_Proteins_prot_ids":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_annot_4/Good_AntiFam_filtered_proteins_gilist":{"sourceIDs":["spurious_annot_2"]}}},"protein_alignment":{"label":"Align reference proteins plane complete workflow","run":"protein_alignment/wf_protein_alignment.cwl","runType":"WORKFLOW","sources":{"protein_alignment":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/taxid":{"sourceIDs":["taxid"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/blastdb_dir":{"sourceIDs":["Create_Genomic_BLASTdb"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/gc_assembly":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/compartments":{"sourceIDs":["bacterial_annot_2"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/tax_sql_file":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#protein_alignment/naming_sqlite":{"sourceIDs":["passdata"]}}},"add_checksum_gbent":{"run":"progs/annot_checksum.cwl","runType":"COMMANDLINETOOL","sources":{"add_checksum_gbent":{"defaultVal":"\\\"annot-gb.ent\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_gbent/t":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_gbent/ifmt":{"defaultVal":"\\\"seq-entry\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_gbent/mode":{"defaultVal":"\\\"add\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#add_checksum_gbent/input":{"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/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/model_path":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/rfam_stockholm":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/16s_blastdb_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_noncoding/23s_blastdb_dir":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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"]}}},"bacterial_mobile_elem":{"label":"Execute CRISPR","run":"bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl","runType":"WORKFLOW","sources":{"bacterial_mobile_elem":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_mobile_elem/go":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_evaluate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#bacterial_mobile_elem/asn_cache":{"sourceIDs":["genomic_source"]}}},"Create_Genomic_BLASTdb":{"label":"gp_makeblastdb","run":"progs/gp_makeblastdb.cwl","runType":"WORKFLOW","sources":{"Create_Genomic_BLASTdb":{"defaultVal":"\\\"nucl\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Create_Genomic_BLASTdb/ids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Create_Genomic_BLASTdb/title":{"defaultVal":"\\\"BLASTdb  created by GPipe\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Create_Genomic_BLASTdb/asn_cache":{"sourceIDs":["genomic_source"]}}},"Prepare_Unannotated_Sequences":{"label":"Prepare Unannotated Sequences","doc":"Note that this implementation skips asn validation steps. Please fix","run":"bacterial_prepare_unannotated.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences":{"sourceIDs":["no_internet"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences/ids":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences/gc_assembly":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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":{"defaultVal":"\\\"annot-wo-checksum.sqn\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/it":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/annotation":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/gc_assembly":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/submit_block_template":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_ent2sqn/contact_as_author_possible":{"sourceIDs":["contact_as_author_possible"]}}},"Generate_Annotation_Reports_gbk":{"label":"asn2flat","run":"progs/asn2flat.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_gbk":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gbk/mode":{"defaultVal":"\\\"entrez\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gbk/type":{"defaultVal":"\\\"seq-entry\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gbk/style":{"defaultVal":"\\\"master\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gbk/gbload":{"defaultVal":"false"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gbk/no_external":{"defaultVal":"true"}}},"Generate_Annotation_Reports_gff":{"label":"gp_annot_format","run":"progs/gp_annot_format.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_gff":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gff/t":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gff/ifmt":{"defaultVal":"\\\"seq-entry\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gff/ofmt":{"defaultVal":"\\\"gff3\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_gff/input":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]}}},"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":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_sqn2gbent/input":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_sqn2gbent/out_name":{"defaultVal":"\\\"annot-gb-wo-checksum.ent\\\""}}},"Final_Bacterial_Package_val_stats":{"label":"val_stats","run":"progs/val_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_val_stats":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_val_stats/annot_val":{"sourceIDs":["Final_Bacterial_Package_std_validation"]}}},"Prepare_Unannotated_Sequences_text":{"label":"asn_translator","run":"progs/asn_translator.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_text":{"defaultVal":"\\\"sequences.text.asn\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_text/input":{"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":{"defaultVal":"\\\"binary\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_asn_cleanup/inp_annotation":{"sourceIDs":["Add_Locus_Tags"]}}},"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/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_proc_annot_stats/it":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_proc_annot_stats/input":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_proc_annot_stats/val_res_den_xml":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_proc_annot_stats/max_unannotated_region":{"defaultVal":"5000"}}},"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/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_xsltproc_asndisc/xml":{"sourceIDs":["Final_Bacterial_Package_std_validation"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_xsltproc_asndisc/output_name":{"defaultVal":"\\\"var_proc_annot_stats.disc.xml\\\""}}},"Generate_Annotation_Reports_nuc_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_nuc_fasta":{"defaultVal":"\\\"annot.fna\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_nuc_fasta/i":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_nuc_fasta/type":{"defaultVal":"\\\"seq-entry\\\""}}},"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":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/it":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/nogenbank":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/annotation":{"sourceIDs":["Final_Bacterial_Package_asn_cleanup"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/master_desc":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_final_bact_asn/submission_mode_genbank":{"defaultVal":"true"}}},"Final_Bacterial_Package_std_validation":{"label":"std_validation","run":"progs/std_validation.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_std_validation":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/ingb":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/inent":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/insqn":{"sourceIDs":["Final_Bacterial_Package_ent2sqn"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/nogenbank":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/annotation":{"sourceIDs":["Final_Bacterial_Package_dumb_down_as_required"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/master_desc":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/exclude_asndisc_codes":{"defaultVal":"\\\"N_RUNS\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/submit_block_template":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_std_validation/submission_mode_genbank":{"defaultVal":"true"}}},"Generate_Annotation_Reports_prot_fasta":{"label":"asn2fasta","run":"progs/asn2fasta.cwl","runType":"COMMANDLINETOOL","sources":{"Generate_Annotation_Reports_prot_fasta":{"sourceIDs":["Final_Bacterial_Package_sqn2gbent"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_prot_fasta/type":{"defaultVal":"\\\"seq-entry\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Generate_Annotation_Reports_prot_fasta/prot_fasta_name":{"defaultVal":"\\\"annot.faa\\\""}}},"Validate_Annotation_collect_annot_stats":{"label":"collect_annot_stats","run":"progs/collect_annot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_collect_annot_stats":{"defaultVal":"\\\"proc_annot_stats.xml\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_collect_annot_stats/input":{"sourceIDs":["Validate_Annotation_bact_univ_prot_stats"]}}},"Final_Bacterial_Package_asndisc_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_asndisc_evaluate":{"sourceIDs":["ignore_all_errors"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_asndisc_evaluate/input":{"sourceIDs":["Final_Bacterial_Package_std_validation"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_asndisc_evaluate/xpath_fail":{"sourceIDs":["xpath_fail_final_asndisc"]}}},"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":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/it":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/input":{"sourceIDs":["Final_Bacterial_Package_final_bact_asn"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/hmm_search":{"sourceIDs":["bacterial_annot_3"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/univ_prot_xml":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/val_res_den_xml":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_bact_univ_prot_stats/annot_request_id":{"defaultVal":"-1"}}},"Validate_Annotation_xsltproc_asnvalidate":{"label":"xsltproc","run":"progs/xsltproc.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_xsltproc_asnvalidate":{"defaultVal":"\\\"var_proc_annot_stats.val.xml\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_xsltproc_asnvalidate/xml":{"sourceIDs":["Final_Bacterial_Package_val_stats"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_xsltproc_asnvalidate/xslt":{"sourceIDs":["passdata"]}}},"Prepare_Unannotated_Sequences_asndisc_cpp":{"label":"asndisc_cpp","run":"progs/asndisc_cpp.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asndisc_cpp":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/P":{"defaultVal":"\\\"t\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/a":{"defaultVal":"\\\"c\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/d":{"defaultVal":"\\\"N_RUNS\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/i":{"sourceIDs":["Prepare_Unannotated_Sequences_text"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/genbank":{"defaultVal":"false"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_cpp/o_output":{"defaultVal":"\\\"sequences.disc.xml\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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":{"defaultVal":"0"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/A":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/R":{"defaultVal":"5"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/U":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/Z":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/a":{"defaultVal":"\\\"e\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/b":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/i":{"sourceIDs":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/v":{"defaultVal":"4"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/y":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate/o_output":{"defaultVal":"\\\"sequences.val\\\""}}},"Validate_Annotation_collect_annot_details":{"label":"collect_annot_stats","run":"progs/collect_annot_stats.cwl","runType":"COMMANDLINETOOL","sources":{"Validate_Annotation_collect_annot_details":{"defaultVal":"\\\"proc_annot_details.xml\\\""},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Validate_Annotation_collect_annot_details/input":{"sourceIDs":["Validate_Annotation_bact_univ_prot_stats"]}}},"Final_Bacterial_Package_asnvalidate_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Final_Bacterial_Package_asnvalidate_evaluate":{"sourceIDs":["ignore_all_errors"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_asnvalidate_evaluate/input":{"sourceIDs":["Final_Bacterial_Package_std_validation"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_asnvalidate_evaluate/xpath_fail":{"sourceIDs":["xpath_fail_final_asnvalidate"]}}},"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":["Final_Bacterial_Package_final_bact_asn"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/it":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/asn_cache":{"sourceIDs":["genomic_source"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/max_x_run":{"defaultVal":"3"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/nogenbank":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/max_x_ratio":{"defaultVal":"1e-01"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/submol_block_json":{"sourceIDs":["submol_block_json"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/partial_cov_threshold":{"defaultVal":"65"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/partial_len_threshold":{"defaultVal":"30"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/submission_mode_genbank":{"defaultVal":"true"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Final_Bacterial_Package_dumb_down_as_required/drop_partial_in_the_middle":{"defaultVal":"true"}}},"Prepare_Unannotated_Sequences_asndisc_evaluate":{"label":"xml_evaluate","run":"progs/xml_evaluate.cwl","runType":"COMMANDLINETOOL","sources":{"Prepare_Unannotated_Sequences_asndisc_evaluate":{"sourceIDs":["xpath_fail_initial_asndisc"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asndisc_evaluate/input":{"sourceIDs":["Prepare_Unannotated_Sequences_asndisc_cpp"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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":["Prepare_Unannotated_Sequences"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/max_size":{"defaultVal":"15000000"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/min_size":{"defaultVal":"300"},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/taxon_db":{"sourceIDs":["passdata"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_pgapx_input_check/ignore_all_errors":{"sourceIDs":["ignore_all_errors"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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":["xpath_fail_initial_asnvalidate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl#Prepare_Unannotated_Sequences_asnvalidate_evaluate/input":{"sourceIDs":["Prepare_Unannotated_Sequences_asnvalidate"]},"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/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    \"xpath_fail_initial_asndisc\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_initial_asndisc\"];\n    \"supplemental_data\" [fillcolor=\"#94DDF4\",label=\"supplemental_data\"];\n    \"ignore_all_errors\" [fillcolor=\"#94DDF4\",label=\"ignore_all_errors\"];\n    \"scatter_gather_nchunks\" [fillcolor=\"#94DDF4\",label=\"scatter_gather_nchunks\"];\n    \"report_usage\" [fillcolor=\"#94DDF4\",label=\"report_usage\"];\n    \"seq_submit\" [fillcolor=\"#94DDF4\",label=\"seq_submit\"];\n    \"no_internet\" [fillcolor=\"#94DDF4\",label=\"no_internet\"];\n    \"gc_assm_name\" [fillcolor=\"#94DDF4\",label=\"gc_assm_name\"];\n    \"xpath_fail_initial_asnvalidate\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_initial_asnvalidate\"];\n    \"submol_block_json\" [fillcolor=\"#94DDF4\",label=\"submol_block_json\"];\n    \"contact_as_author_possible\" [fillcolor=\"#94DDF4\",label=\"contact_as_author_possible\"];\n    \"taxid\" [fillcolor=\"#94DDF4\",label=\"taxid\"];\n    \"blast_rules_db\" [fillcolor=\"#94DDF4\",label=\"blast_rules_db\"];\n    \"dbname\" [fillcolor=\"#94DDF4\",label=\"dbname\"];\n    \"xpath_fail_final_asnvalidate\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_final_asnvalidate\"];\n    \"go\" [fillcolor=\"#94DDF4\",label=\"go\"];\n    \"locus_tag_prefix\" [fillcolor=\"#94DDF4\",label=\"locus_tag_prefix\"];\n    \"xpath_fail_final_asndisc\" [fillcolor=\"#94DDF4\",label=\"xpath_fail_final_asndisc\"];\n    \"entries\" [fillcolor=\"#94DDF4\",label=\"entries\"];\n    \"blast_hits_cache_data\" [fillcolor=\"#94DDF4\",label=\"blast_hits_cache_data\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"sqn\" [fillcolor=\"#94DDF4\",label=\"sqn\"];\n    \"proc_annot_stats\" [fillcolor=\"#94DDF4\",label=\"proc_annot_stats\"];\n    \"gff\" [fillcolor=\"#94DDF4\",label=\"gff\"];\n    \"nucleotide_fasta\" [fillcolor=\"#94DDF4\",label=\"nucleotide_fasta\"];\n    \"protein_fasta\" [fillcolor=\"#94DDF4\",label=\"protein_fasta\"];\n    \"gbent\" [fillcolor=\"#94DDF4\",label=\"gbent\"];\n    \"gbk\" [fillcolor=\"#94DDF4\",label=\"gbk\"];\n  }\n  \"Validate_Annotation_xsltproc_asndisc\" [label=\"xsltproc\"];\n  \"spurious_annot_2\" [label=\"spurious_annot pass2\", fillcolor=\"#F3CEA1\"];\n  \"Cache_Entrez_Gene\" [label=\"Cache Entrez Gene\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"asnvalidate\"];\n  \"bacterial_annot_4\" [label=\"Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"asndisc_cpp\"];\n  \"bacterial_mobile_elem\" [label=\"Execute CRISPR\", fillcolor=\"#F3CEA1\"];\n  \"passdata\" [label=\"Split input directory into subpath flows\"];\n  \"Prepare_Unannotated_Sequences_text\" [label=\"asn_translator\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"xml_evaluate\"];\n  \"Validate_Annotation_proc_annot_stats\" [label=\"proc_annot_stats\"];\n  \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xsltproc\"];\n  \"Final_Bacterial_Package_std_validation\" [label=\"std_validation\"];\n  \"Prepare_Unannotated_Sequences\" [label=\"Prepare Unannotated Sequences\"];\n  \"blast_hits_cache_data_split_dir\" [label=\"Split input directory into subpath flows\"];\n  \"spurious_annot_1\" [label=\"spurious_annot\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_ent2sqn\" [label=\"ent2sqn\"];\n  \"Validate_Annotation_collect_annot_details\" [label=\"collect_annot_stats\"];\n  \"Generate_Annotation_Reports_gff\" [label=\"gp_annot_format\"];\n  \"Validate_Annotation_bact_univ_prot_stats\" [label=\"bact_univ_prot_stats\"];\n  \"bacterial_annot\" [label=\"Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"pgapx_input_check\"];\n  \"bacterial_annot_3\" [label=\"Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"xml_evaluate\"];\n  \"Final_Bacterial_Package_final_bact_asn\" [label=\"final_bact_asn\"];\n  \"add_checksum_sqn\" [label=\"add_checksum_sqn\"];\n  \"ping_start\" [label=\"pinger\"];\n  \"Final_Bacterial_Package_sqn2gbent\" [label=\"sqn2gbent\"];\n  \"Generate_Annotation_Reports_gbk\" [label=\"asn2flat\"];\n  \"add_checksum_gbent\" [label=\"add_checksum_gbent\"];\n  \"bacterial_noncoding\" [label=\"Non-Coding Bacterial Genes\", fillcolor=\"#F3CEA1\"];\n  \"ping_stop\" [label=\"pinger\"];\n  \"bacterial_annot_2\" [label=\"Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)\", fillcolor=\"#F3CEA1\"];\n  \"genomic_source\" [label=\"Create Genomic Collection for Bacterial Pipeline, ASN.1 input\", fillcolor=\"#F3CEA1\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"xml_evaluate\"];\n  \"Generate_Annotation_Reports_nuc_fasta\" [label=\"asn2fasta\"];\n  \"Validate_Annotation_collect_annot_stats\" [label=\"collect_annot_stats\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"dumb_down_as_required\"];\n  \"bacterial_ncrna\" [label=\"Run genomic CMsearch (Rfam rRNA)\", fillcolor=\"#F3CEA1\"];\n  \"Add_Locus_Tags\" [label=\"add_locus_tags\"];\n  \"Create_Genomic_BLASTdb\" [label=\"gp_makeblastdb\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_val_stats\" [label=\"val_stats\"];\n  \"bacterial_trna\" [label=\"Run tRNAScan\", fillcolor=\"#F3CEA1\"];\n  \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"xml_evaluate\"];\n  \"genus_list_file2ints\" [label=\"genus_list_file2ints\"];\n  \"protein_alignment\" [label=\"Align reference proteins plane complete workflow\", fillcolor=\"#F3CEA1\"];\n  \"Generate_Annotation_Reports_prot_fasta\" [label=\"asn2fasta\"];\n  \"Final_Bacterial_Package_asn_cleanup\" [label=\"asn_cleanup\"];\n  \"passdata\" -> \"Validate_Annotation_xsltproc_asndisc\" [label=\"xslt\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Validate_Annotation_xsltproc_asndisc\" [label=\"xml\"];\n  \"default1\" -> \"Validate_Annotation_xsltproc_asndisc\" [label=\"output_name\"];\n  \"default1\" [label=\"\\\"var_proc_annot_stats.disc.xml\\\"\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"spurious_annot_2\" [label=\"AntiFamLib\"];\n  \"bacterial_annot_3\" -> \"spurious_annot_2\" [label=\"Extract_Model_Proteins_proteins\"];\n  \"scatter_gather_nchunks\" -> \"spurious_annot_2\" [label=\"scatter_gather_nchunks\"];\n  \"genomic_source\" -> \"spurious_annot_2\" [label=\"sequence_cache\"];\n  \"bacterial_annot_3\" -> \"spurious_annot_2\" [label=\"Extract_Model_Proteins_lds2\"];\n  \"bacterial_annot_3\" -> \"spurious_annot_2\" [label=\"Extract_Model_Proteins_seqids\"];\n  \"bacterial_annot_3\" -> \"spurious_annot_2\" [label=\"Run_GeneMark_models\"];\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  \"default2\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"Q\"];\n  \"default2\" [label=\"0\", fillcolor=\"#D5AEFC\"];\n  \"default3\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"o_output\"];\n  \"default3\" [label=\"\\\"sequences.val\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default4\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"R\"];\n  \"default4\" [label=\"5\", fillcolor=\"#D5AEFC\"];\n  \"default5\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"v\"];\n  \"default5\" [label=\"4\", fillcolor=\"#D5AEFC\"];\n  \"default6\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"y\"];\n  \"default6\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default7\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"U\"];\n  \"default7\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default8\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"a\"];\n  \"default8\" [label=\"\\\"e\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default9\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"b\"];\n  \"default9\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default10\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"A\"];\n  \"default10\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default11\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"Z\"];\n  \"default11\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_asnvalidate\" [label=\"i\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"uniColl_cache\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"identification_db_dir\"];\n  \"bacterial_annot_3\" -> \"bacterial_annot_4\" [label=\"wp_assignments\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"naming_blast_db\"];\n  \"bacterial_annot_3\" -> \"bacterial_annot_4\" [label=\"hmm_assignments\"];\n  \"spurious_annot_2\" -> \"bacterial_annot_4\" [label=\"annotation\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"taxon_db\"];\n  \"blast_hits_cache_data_split_dir\" -> \"bacterial_annot_4\" [label=\"blast_hits_cache\"];\n  \"bacterial_annot_3\" -> \"bacterial_annot_4\" [label=\"Extract_Model_Proteins_prot_ids\"];\n  \"spurious_annot_2\" -> \"bacterial_annot_4\" [label=\"Good_AntiFam_filtered_proteins_gilist\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"CDDdata\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"CDDdata2\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"blast_rules_db_dir\"];\n  \"blast_rules_db\" -> \"bacterial_annot_4\" [label=\"blast_rules_db\"];\n  \"bacterial_annot_3\" -> \"bacterial_annot_4\" [label=\"proteins\"];\n  \"bacterial_annot_3\" -> \"bacterial_annot_4\" [label=\"lds2\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_4\" [label=\"scatter_gather_nchunks\"];\n  \"taxid\" -> \"bacterial_annot_4\" [label=\"taxid\"];\n  \"genomic_source\" -> \"bacterial_annot_4\" [label=\"sequence_cache\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"naming_sqlite\"];\n  \"genus_list_file2ints\" -> \"bacterial_annot_4\" [label=\"genus_list\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"defline_cleanup_rules\"];\n  \"passdata\" -> \"bacterial_annot_4\" [label=\"thresholds\"];\n  \"default12\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"XML\"];\n  \"default12\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default13\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"P\"];\n  \"default13\" [label=\"\\\"t\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default14\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"genbank\"];\n  \"default14\" [label=\"false\", fillcolor=\"#D5AEFC\"];\n  \"default15\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default15\" [label=\"\\\"AUTODEF_USER_OBJECT\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default16\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default16\" [label=\"\\\"TAX_LOOKUP_MISSING\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default17\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default17\" [label=\"\\\"SHORT_PROT_SEQUENCES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default18\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default18\" [label=\"\\\"BAD_BGPIPE_QUALS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default19\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default19\" [label=\"\\\"PARTIAL_CDS_COMPLETE_SEQUENCE\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default20\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default20\" [label=\"\\\"OVERLAPPING_CDS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default21\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default21\" [label=\"\\\"EXTRA_GENES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default22\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default22\" [label=\"\\\"FEATURE_LIST\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default23\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default23\" [label=\"\\\"BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default24\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default24\" [label=\"\\\"TAX_LOOKUP_MISMATCH\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default25\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default25\" [label=\"\\\"COMMENT_PRESENT\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default26\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default26\" [label=\"\\\"OVERLAPPING_GENES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default27\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default27\" [label=\"\\\"FLATFILE_FIND\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default28\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default28\" [label=\"\\\"MISSING_AFFIL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default29\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"d\"];\n  \"default29\" [label=\"\\\"N_RUNS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"asn_cache\"];\n  \"default30\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"a\"];\n  \"default30\" [label=\"\\\"c\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default31\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"o_output\"];\n  \"default31\" [label=\"\\\"sequences.disc.xml\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Prepare_Unannotated_Sequences_text\" -> \"Prepare_Unannotated_Sequences_asndisc_cpp\" [label=\"i\"];\n  \"genomic_source\" -> \"bacterial_mobile_elem\" [label=\"seqids\"];\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  \"supplemental_data\" -> \"passdata\" [label=\"data\"];\n  \"default32\" -> \"Prepare_Unannotated_Sequences_text\" [label=\"output_output\"];\n  \"default32\" [label=\"\\\"sequences.text.asn\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_text\" [label=\"input\"];\n  \"xpath_fail_initial_asnvalidate\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"xpath_fail\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"input\"];\n  \"ignore_all_errors\" -> \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" [label=\"ignore_all_errors\"];\n  \"passdata\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"univ_prot_xml\"];\n  \"passdata\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"val_res_den_xml\"];\n  \"default33\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"max_unannotated_region\"];\n  \"default33\" [label=\"5000\", fillcolor=\"#D5AEFC\"];\n  \"default34\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"it\"];\n  \"default34\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Validate_Annotation_proc_annot_stats\" [label=\"input\"];\n  \"default35\" -> \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"output_name\"];\n  \"default35\" [label=\"\\\"var_proc_annot_stats.val.xml\\\"\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xslt\"];\n  \"Final_Bacterial_Package_val_stats\" -> \"Validate_Annotation_xsltproc_asnvalidate\" [label=\"xml\"];\n  \"default36\" -> \"Final_Bacterial_Package_std_validation\" [label=\"it\"];\n  \"default36\" [label=\"true\", fillcolor=\"#D5AEFC\"];\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  \"Prepare_Unannotated_Sequences\" -> \"Final_Bacterial_Package_std_validation\" [label=\"master_desc\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_std_validation\" [label=\"submit_block_template\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"Final_Bacterial_Package_std_validation\" [label=\"insqn\"];\n  \"default37\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default37\" [label=\"\\\"AUTODEF_USER_OBJECT\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default38\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default38\" [label=\"\\\"BAD_LOCUS_TAG_FORMAT\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default39\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default39\" [label=\"\\\"TAX_LOOKUP_MISSING\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default40\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default40\" [label=\"\\\"SHORT_PROT_SEQUENCES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default41\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default41\" [label=\"\\\"BAD_BGPIPE_QUALS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default42\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default42\" [label=\"\\\"PARTIAL_CDS_COMPLETE_SEQUENCE\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default43\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default43\" [label=\"\\\"OVERLAPPING_CDS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default44\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default44\" [label=\"\\\"EXTRA_GENES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default45\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default45\" [label=\"\\\"FEATURE_LIST\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default46\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default46\" [label=\"\\\"BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default47\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default47\" [label=\"\\\"TAX_LOOKUP_MISMATCH\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default48\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default48\" [label=\"\\\"COMMENT_PRESENT\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default49\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default49\" [label=\"\\\"OVERLAPPING_GENES\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default50\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default50\" [label=\"\\\"FLATFILE_FIND\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default51\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default51\" [label=\"\\\"MISSING_AFFIL\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default52\" -> \"Final_Bacterial_Package_std_validation\" [label=\"exclude_asndisc_codes\"];\n  \"default52\" [label=\"\\\"N_RUNS\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Final_Bacterial_Package_std_validation\" [label=\"ingb\"];\n  \"default53\" -> \"Final_Bacterial_Package_std_validation\" [label=\"nogenbank\"];\n  \"default53\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default54\" -> \"Final_Bacterial_Package_std_validation\" [label=\"submission_mode_genbank\"];\n  \"default54\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_std_validation\" [label=\"asn_cache\"];\n  \"no_internet\" -> \"Prepare_Unannotated_Sequences\" [label=\"no_internet\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"asn_cache\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"submit_block\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"gc_assembly\"];\n  \"genomic_source\" -> \"Prepare_Unannotated_Sequences\" [label=\"ids\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences\" [label=\"taxon_db\"];\n  \"blast_hits_cache_data\" -> \"blast_hits_cache_data_split_dir\" [label=\"data\"];\n  \"bacterial_annot\" -> \"spurious_annot_1\" [label=\"Extract_ORF_Proteins_seqids\"];\n  \"genomic_source\" -> \"spurious_annot_1\" [label=\"sequence_cache\"];\n  \"scatter_gather_nchunks\" -> \"spurious_annot_1\" [label=\"scatter_gather_nchunks\"];\n  \"bacterial_annot\" -> \"spurious_annot_1\" [label=\"Extract_ORF_Proteins_proteins\"];\n  \"bacterial_annot\" -> \"spurious_annot_1\" [label=\"Extract_ORF_Proteins_lds2\"];\n  \"passdata\" -> \"spurious_annot_1\" [label=\"AntiFamLib\"];\n  \"default55\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"output_impl\"];\n  \"default55\" [label=\"\\\"annot-wo-checksum.sqn\\\"\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"asn_cache\"];\n  \"contact_as_author_possible\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"contact_as_author_possible\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"submit_block_template\"];\n  \"default56\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"it\"];\n  \"default56\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"gc_assembly\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Final_Bacterial_Package_ent2sqn\" [label=\"annotation\"];\n  \"default57\" -> \"Validate_Annotation_collect_annot_details\" [label=\"output_name\"];\n  \"default57\" [label=\"\\\"proc_annot_details.xml\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Validate_Annotation_proc_annot_stats\" -> \"Validate_Annotation_collect_annot_details\" [label=\"input\"];\n  \"Validate_Annotation_bact_univ_prot_stats\" -> \"Validate_Annotation_collect_annot_details\" [label=\"input\"];\n  \"default58\" -> \"Generate_Annotation_Reports_gff\" [label=\"exclude_external\"];\n  \"default58\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default59\" -> \"Generate_Annotation_Reports_gff\" [label=\"t\"];\n  \"default59\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default60\" -> \"Generate_Annotation_Reports_gff\" [label=\"ifmt\"];\n  \"default60\" [label=\"\\\"seq-entry\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default61\" -> \"Generate_Annotation_Reports_gff\" [label=\"ofmt\"];\n  \"default61\" [label=\"\\\"gff3\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_dumb_down_as_required\" -> \"Generate_Annotation_Reports_gff\" [label=\"input\"];\n  \"bacterial_annot_3\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"hmm_search_proteins\"];\n  \"Final_Bacterial_Package_final_bact_asn\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"input\"];\n  \"passdata\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"univ_prot_xml\"];\n  \"default62\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"annot_request_id\"];\n  \"default62\" [label=\"-1\", fillcolor=\"#D5AEFC\"];\n  \"default63\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"it\"];\n  \"default63\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"bacterial_annot_3\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"hmm_search\"];\n  \"passdata\" -> \"Validate_Annotation_bact_univ_prot_stats\" [label=\"val_res_den_xml\"];\n  \"Prepare_Unannotated_Sequences\" -> \"bacterial_annot\" [label=\"inseq\"];\n  \"genomic_source\" -> \"bacterial_annot\" [label=\"asn_cache\"];\n  \"bacterial_noncoding\" -> \"bacterial_annot\" [label=\"Generate_16S_rRNA_Annotation_annotation\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"genemark_path\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"uniColl_cache\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"naming_sqlite\"];\n  \"bacterial_noncoding\" -> \"bacterial_annot\" [label=\"Post_process_CMsearch_annotations_annots_5S\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"selenoproteins\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"hmms_tab\"];\n  \"bacterial_trna\" -> \"bacterial_annot\" [label=\"trna_annots\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot\" [label=\"scatter_gather_nchunks\"];\n  \"bacterial_ncrna\" -> \"bacterial_annot\" [label=\"ncrna_annots\"];\n  \"default64\" -> \"bacterial_annot\" [label=\"nogenbank\"];\n  \"default64\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"hmm_path\"];\n  \"passdata\" -> \"bacterial_annot\" [label=\"thresholds\"];\n  \"bacterial_noncoding\" -> \"bacterial_annot\" [label=\"Generate_23S_rRNA_Annotation_annotation\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_annot\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_annot\" [label=\"go\"];\n  \"bacterial_mobile_elem\" -> \"bacterial_annot\" [label=\"Execute_CRISPRs_annots\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"input\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"taxon_db\"];\n  \"ignore_all_errors\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"ignore_all_errors\"];\n  \"default65\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"min_size\"];\n  \"default65\" [label=\"300\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"species_genome_size\"];\n  \"default66\" -> \"Prepare_Unannotated_Sequences_pgapx_input_check\" [label=\"max_size\"];\n  \"default66\" [label=\"15000000\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"selenoproteins\"];\n  \"bacterial_annot\" -> \"bacterial_annot_3\" [label=\"models1\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"naming_sqlite\"];\n  \"Prepare_Unannotated_Sequences\" -> \"bacterial_annot_3\" [label=\"raw_seqs\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_3\" [label=\"scatter_gather_nchunks\"];\n  \"protein_alignment\" -> \"bacterial_annot_3\" [label=\"prot_aligns\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"naming_hmms_combined\"];\n  \"bacterial_annot\" -> \"bacterial_annot_3\" [label=\"annotation\"];\n  \"bacterial_annot\" -> \"bacterial_annot_3\" [label=\"hmm_aligns\"];\n  \"genomic_source\" -> \"bacterial_annot_3\" [label=\"sequence_cache\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"wp_hashes\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"thresholds\"];\n  \"bacterial_annot\" -> \"bacterial_annot_3\" [label=\"hmm_params\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"taxon_db\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"genemark_path\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"uniColl_cache\"];\n  \"passdata\" -> \"bacterial_annot_3\" [label=\"hmms_tab\"];\n  \"ignore_all_errors\" -> \"Final_Bacterial_Package_asnvalidate_evaluate\" [label=\"ignore_all_errors\"];\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  \"genomic_source\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"gc_assembly\"];\n  \"Final_Bacterial_Package_asn_cleanup\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"annotation\"];\n  \"default67\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"submission_mode_genbank\"];\n  \"default67\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default68\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"nogenbank\"];\n  \"default68\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"Prepare_Unannotated_Sequences\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"master_desc\"];\n  \"default69\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"it\"];\n  \"default69\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_final_bact_asn\" [label=\"asn_cache\"];\n  \"default70\" -> \"add_checksum_sqn\" [label=\"output_name\"];\n  \"default70\" [label=\"\\\"annot.sqn\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default71\" -> \"add_checksum_sqn\" [label=\"t\"];\n  \"default71\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default72\" -> \"add_checksum_sqn\" [label=\"mode\"];\n  \"default72\" [label=\"\\\"add\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"add_checksum_sqn\" [label=\"input\"];\n  \"default73\" -> \"add_checksum_sqn\" [label=\"ifmt\"];\n  \"default73\" [label=\"\\\"seq-submit\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default74\" -> \"ping_start\" [label=\"workflow\"];\n  \"default74\" [label=\"\\\"pgap\\\"\", fillcolor=\"#D5AEFC\"];\n  \"gc_assm_name\" -> \"ping_start\" [label=\"instring\"];\n  \"default75\" -> \"ping_start\" [label=\"state\"];\n  \"default75\" [label=\"\\\"start\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default76\" -> \"ping_start\" [label=\"make_uuid\"];\n  \"default76\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"report_usage\" -> \"ping_start\" [label=\"report_usage\"];\n  \"default77\" -> \"Final_Bacterial_Package_sqn2gbent\" [label=\"it\"];\n  \"default77\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default78\" -> \"Final_Bacterial_Package_sqn2gbent\" [label=\"out_name\"];\n  \"default78\" [label=\"\\\"annot-gb-wo-checksum.ent\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_ent2sqn\" -> \"Final_Bacterial_Package_sqn2gbent\" [label=\"input\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_gbk\" [label=\"input\"];\n  \"default79\" -> \"Generate_Annotation_Reports_gbk\" [label=\"type\"];\n  \"default79\" [label=\"\\\"seq-entry\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default80\" -> \"Generate_Annotation_Reports_gbk\" [label=\"style\"];\n  \"default80\" [label=\"\\\"master\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default81\" -> \"Generate_Annotation_Reports_gbk\" [label=\"no_external\"];\n  \"default81\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default82\" -> \"Generate_Annotation_Reports_gbk\" [label=\"mode\"];\n  \"default82\" [label=\"\\\"entrez\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default83\" -> \"Generate_Annotation_Reports_gbk\" [label=\"gbload\"];\n  \"default83\" [label=\"false\", fillcolor=\"#D5AEFC\"];\n  \"default84\" -> \"add_checksum_gbent\" [label=\"output_name\"];\n  \"default84\" [label=\"\\\"annot-gb.ent\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"add_checksum_gbent\" [label=\"input\"];\n  \"default85\" -> \"add_checksum_gbent\" [label=\"t\"];\n  \"default85\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default86\" -> \"add_checksum_gbent\" [label=\"mode\"];\n  \"default86\" [label=\"\\\"add\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default87\" -> \"add_checksum_gbent\" [label=\"ifmt\"];\n  \"default87\" [label=\"\\\"seq-entry\\\"\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"bacterial_noncoding\" [label=\"seqids\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"23s_blastdb_dir\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_noncoding\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_noncoding\" [label=\"go\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"model_path\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"rfam_amendments\"];\n  \"genomic_source\" -> \"bacterial_noncoding\" [label=\"asn_cache\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"rfam_stockholm\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"taxon_db\"];\n  \"passdata\" -> \"bacterial_noncoding\" [label=\"16s_blastdb_dir\"];\n  \"default88\" -> \"ping_stop\" [label=\"state\"];\n  \"default88\" [label=\"\\\"stop\\\"\", fillcolor=\"#D5AEFC\"];\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_gbk\" -> \"ping_stop\" [label=\"infile\"];\n  \"Generate_Annotation_Reports_prot_fasta\" -> \"ping_stop\" [label=\"infile\"];\n  \"default89\" -> \"ping_stop\" [label=\"workflow\"];\n  \"default89\" [label=\"\\\"pgap\\\"\", fillcolor=\"#D5AEFC\"];\n  \"ping_start\" -> \"ping_stop\" [label=\"uuid_in\"];\n  \"report_usage\" -> \"ping_stop\" [label=\"report_usage\"];\n  \"genus_list_file2ints\" -> \"bacterial_annot_2\" [label=\"genus_list\"];\n  \"blast_hits_cache_data_split_dir\" -> \"bacterial_annot_2\" [label=\"blast_hits_cache\"];\n  \"bacterial_annot\" -> \"bacterial_annot_2\" [label=\"prot_ids_B1\"];\n  \"bacterial_annot\" -> \"bacterial_annot_2\" [label=\"prot_ids_A\"];\n  \"scatter_gather_nchunks\" -> \"bacterial_annot_2\" [label=\"scatter_gather_nchunks\"];\n  \"taxid\" -> \"bacterial_annot_2\" [label=\"taxid\"];\n  \"passdata\" -> \"bacterial_annot_2\" [label=\"taxon_db\"];\n  \"spurious_annot_1\" -> \"bacterial_annot_2\" [label=\"prot_ids_B2\"];\n  \"blast_rules_db\" -> \"bacterial_annot_2\" [label=\"blast_rules_db\"];\n  \"passdata\" -> \"bacterial_annot_2\" [label=\"identification_db_dir\"];\n  \"bacterial_annot\" -> \"bacterial_annot_2\" [label=\"proteins\"];\n  \"bacterial_annot\" -> \"bacterial_annot_2\" [label=\"lds2\"];\n  \"passdata\" -> \"bacterial_annot_2\" [label=\"unicoll_cache\"];\n  \"passdata\" -> \"bacterial_annot_2\" [label=\"blast_rules_db_dir\"];\n  \"genomic_source\" -> \"bacterial_annot_2\" [label=\"sequence_cache\"];\n  \"bacterial_annot\" -> \"bacterial_annot_2\" [label=\"annotation\"];\n  \"ping_start\" -> \"genomic_source\" [label=\"gc_assm_name\"];\n  \"entries\" -> \"genomic_source\" [label=\"entries\"];\n  \"seq_submit\" -> \"genomic_source\" [label=\"seq_submit\"];\n  \"passdata\" -> \"genomic_source\" [label=\"taxon_db\"];\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  \"Prepare_Unannotated_Sequences_asndisc_cpp\" -> \"Prepare_Unannotated_Sequences_asndisc_evaluate\" [label=\"input\"];\n  \"default90\" -> \"Generate_Annotation_Reports_nuc_fasta\" [label=\"nuc_fasta_name\"];\n  \"default90\" [label=\"\\\"annot.fna\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default91\" -> \"Generate_Annotation_Reports_nuc_fasta\" [label=\"type\"];\n  \"default91\" [label=\"\\\"seq-entry\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_nuc_fasta\" [label=\"i\"];\n  \"default92\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"output_name\"];\n  \"default92\" [label=\"\\\"proc_annot_stats.xml\\\"\", fillcolor=\"#D5AEFC\"];\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  \"Validate_Annotation_bact_univ_prot_stats\" -> \"Validate_Annotation_collect_annot_stats\" [label=\"input\"];\n  \"Final_Bacterial_Package_final_bact_asn\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"annotation\"];\n  \"submol_block_json\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"submol_block_json\"];\n  \"default93\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"nogenbank\"];\n  \"default93\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default94\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"submission_mode_genbank\"];\n  \"default94\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default95\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"max_x_run\"];\n  \"default95\" [label=\"3\", fillcolor=\"#D5AEFC\"];\n  \"default96\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"it\"];\n  \"default96\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default97\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"max_x_ratio\"];\n  \"default97\" [label=\"1e-01\", fillcolor=\"#D5AEFC\"];\n  \"default98\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"partial_cov_threshold\"];\n  \"default98\" [label=\"65\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"asn_cache\"];\n  \"default99\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"drop_partial_in_the_middle\"];\n  \"default99\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"default100\" -> \"Final_Bacterial_Package_dumb_down_as_required\" [label=\"partial_len_threshold\"];\n  \"default100\" [label=\"30\", fillcolor=\"#D5AEFC\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"model_path\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"taxon_db\"];\n  \"genomic_source\" -> \"bacterial_ncrna\" [label=\"seqids\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"rfam_stockholm\"];\n  \"passdata\" -> \"bacterial_ncrna\" [label=\"rfam_amendments\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_ncrna\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_ncrna\" [label=\"go\"];\n  \"genomic_source\" -> \"bacterial_ncrna\" [label=\"asn_cache\"];\n  \"bacterial_annot_4\" -> \"Add_Locus_Tags\" [label=\"input\"];\n  \"dbname\" -> \"Add_Locus_Tags\" [label=\"dbname\"];\n  \"locus_tag_prefix\" -> \"Add_Locus_Tags\" [label=\"locus_tag_prefix\"];\n  \"default101\" -> \"Create_Genomic_BLASTdb\" [label=\"dbtype\"];\n  \"default101\" [label=\"\\\"nucl\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default102\" -> \"Create_Genomic_BLASTdb\" [label=\"title\"];\n  \"default102\" [label=\"\\\"BLASTdb  created by GPipe\\\"\", fillcolor=\"#D5AEFC\"];\n  \"genomic_source\" -> \"Create_Genomic_BLASTdb\" [label=\"ids\"];\n  \"genomic_source\" -> \"Create_Genomic_BLASTdb\" [label=\"asn_cache\"];\n  \"default103\" -> \"Final_Bacterial_Package_val_stats\" [label=\"c_toolkit\"];\n  \"default103\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"Final_Bacterial_Package_std_validation\" -> \"Final_Bacterial_Package_val_stats\" [label=\"annot_val\"];\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  \"taxid\" -> \"bacterial_trna\" [label=\"taxid\"];\n  \"genomic_source\" -> \"bacterial_trna\" [label=\"seqids\"];\n  \"Prepare_Unannotated_Sequences_asnvalidate_evaluate\" -> \"bacterial_trna\" [label=\"go\"];\n  \"Prepare_Unannotated_Sequences_asndisc_evaluate\" -> \"bacterial_trna\" [label=\"go\"];\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  \"xpath_fail_final_asndisc\" -> \"Final_Bacterial_Package_asndisc_evaluate\" [label=\"xpath_fail\"];\n  \"blast_hits_cache_data_split_dir\" -> \"genus_list_file2ints\" [label=\"input\"];\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=\"gc_assembly\"];\n  \"passdata\" -> \"protein_alignment\" [label=\"tax_sql_file\"];\n  \"Create_Genomic_BLASTdb\" -> \"protein_alignment\" [label=\"blastdb_dir\"];\n  \"genomic_source\" -> \"protein_alignment\" [label=\"asn_cache\"];\n  \"passdata\" -> \"protein_alignment\" [label=\"naming_sqlite\"];\n  \"taxid\" -> \"protein_alignment\" [label=\"taxid\"];\n  \"bacterial_annot_2\" -> \"protein_alignment\" [label=\"compartments\"];\n  \"Final_Bacterial_Package_sqn2gbent\" -> \"Generate_Annotation_Reports_prot_fasta\" [label=\"i\"];\n  \"default104\" -> \"Generate_Annotation_Reports_prot_fasta\" [label=\"type\"];\n  \"default104\" [label=\"\\\"seq-entry\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default105\" -> \"Generate_Annotation_Reports_prot_fasta\" [label=\"prot_fasta_name\"];\n  \"default105\" [label=\"\\\"annot.faa\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default106\" -> \"Final_Bacterial_Package_asn_cleanup\" [label=\"serial\"];\n  \"default106\" [label=\"\\\"binary\\\"\", fillcolor=\"#D5AEFC\"];\n  \"Add_Locus_Tags\" -> \"Final_Bacterial_Package_asn_cleanup\" [label=\"inp_annotation\"];\n  \"add_checksum_sqn\" -> \"sqn\";\n  \"Validate_Annotation_proc_annot_stats\" -> \"proc_annot_stats\";\n  \"Generate_Annotation_Reports_gff\" -> \"gff\";\n  \"Generate_Annotation_Reports_nuc_fasta\" -> \"nucleotide_fasta\";\n  \"Generate_Annotation_Reports_prot_fasta\" -> \"protein_fasta\";\n  \"add_checksum_gbent\" -> \"gbent\";\n  \"Generate_Annotation_Reports_gbk\" -> \"gbk\";\n}\n","licenseLink":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/LICENSE.md","permalink":"https://w3id.org/cwl/view/git/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","visualisationPng":"/graph/png/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","visualisationSvg":"/graph/svg/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","roBundle":"/robundle/github.com/ncbi/pgap/blob/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/wf_common.cwl","licenseName":"https://raw.githubusercontent.com/ncbi/pgap/4def84df33963fc9ac9d5c5f804b911d01a0d9ad/LICENSE.md"}