#!/usr/bin/env cwl-runner label: "PGAP Pipeline" cwlVersion: v1.0 class: Workflow doc: PGAP pipeline for external usage, powered via containers requirements: - class: SubworkflowFeatureRequirement - class: MultipleInputFeatureRequirement inputs: # # User specific input # entries: File? seq_submit: File? taxid: int gc_assm_name: string locus_tag_prefix: string? dbname: string? report_usage: boolean # # User independent, static input # blast_rules_db: type: string default: blast_rules_db scatter_gather_nchunks: type: string default: '1' supplemental_data: type: Directory default: class: Directory location: input submol_block_json: type: File steps: ping_start: run: progs/pinger.cwl in: report_usage: report_usage make_uuid: default: true state: default: "start" workflow: default: "pgap" instring: gc_assm_name out: [stdout, outstring, uuid_out] passdata: in: data: supplemental_data run: class: ExpressionTool requirements: InlineJavascriptRequirement: {} inputs: data: type: Directory expression: | ${ var r = {}; var l = inputs.data.listing; var n = l.length; for (var i = 0; i < n; i++) { switch (l[i].basename) { case '16S_rRNA': r['16s_blastdb_dir'] = l[i]; break; case '23S_rRNA': r['23s_blastdb_dir'] = l[i]; break; case 'RF00001.cm': r['5s_model_path'] = l[i]; break; case 'AntiFamLib': r['AntiFamLib'] = l[i]; break; case 'asn2pas.xsl': r['asn2pas_xsl'] = l[i]; break; case 'CDD2': r['CDDdata'] = l[i]; break; case 'cdd_add': r['CDDdata2'] = l[i]; break; case 'product_rules.prt': r['defline_cleanup_rules'] = l[i]; break; case 'gene_master.ini': r['gene_master_ini'] = l[i]; break; case 'GeneMark': r['genemark_path'] = l[i]; break; case 'rfam-amendments.xml': r['rfam_amendments'] = l[i]; break; case 'Rfam.selected1.cm': r['rfam_model_path'] = l[i]; break; case 'Rfam.seed': r['rfam_stockholm'] = l[i]; break; case 'selenoproteins': r['selenoproteins'] = l[i]; break; case 'thresholds.xml': r['thresholds'] = l[i]; break; case 'species_genome_size.txt': r['species_genome_size'] = l[i]; break; case 'uniColl_path': var ul = l[i].listing; var un = ul.length; for (var j = 0; j < un; j++) { switch (ul[j].basename) { case 'blast_dir': r['blast_rules_db_dir'] = ul[j]; r['naming_blast_db'] = ul[j]; break; case 'real_hmms': r['hmm_path'] = ul[j]; break; case 'real_hmms.tab': r['hmms_tab'] = ul[j]; break; case 'naming_hmms': r['naming_hmms_combined'] = ul[j]; break; case 'naming_hmms.tab': r['naming_hmms_tab'] = ul[j]; break; case 'naming.sqlite': r['naming_sqlite'] = ul[j]; break; case 'taxonomy.sqlite3': r['taxon_db'] = ul[j]; break; case 'cache': r['uniColl_cache'] = ul[j]; break; case 'universal.xml': r['univ_prot_xml'] = ul[j]; break; case 'wp-hashes.sqlite': r['wp_hashes'] = ul[j]; break; } } break; case 'validation-results.xml': r['val_res_den_xml'] = l[i]; break; } } return r; } outputs: 16s_blastdb_dir: type: Directory 23s_blastdb_dir: type: Directory 5s_model_path: type: File AntiFamLib: type: Directory asn2pas_xsl: type: File blast_rules_db_dir: type: Directory CDDdata: # ${GP_HOME}/third-party/data/CDD/cdd - this is rpsblastdb type: Directory CDDdata2: # ${GP_HOME}/third-party/data/cdd_add type: Directory defline_cleanup_rules: # defline_cleanup_rules # ${GP_HOME}/etc/product_rules.prt type: File gene_master_ini: type: File genemark_path: type: Directory hmm_path: type: Directory hmms_tab: type: File naming_blast_db: # NamingDatabase type: Directory naming_hmms_combined: # ${GP_HOME}/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming_hmms_combined.mft type: Directory naming_hmms_tab: type: File naming_sqlite: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/uniColl/ver-3.2/naming.sqlite type: File rfam_amendments: type: File rfam_model_path: type: File rfam_stockholm: type: File selenoproteins: # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/Selenoproteins/selenoproteins, it's blastdb type: Directory species_genome_size: type: File taxon_db: type: File thresholds: type: File uniColl_cache: type: Directory univ_prot_xml: type: File val_res_den_xml: type: File wp_hashes: type: File out: - 16s_blastdb_dir - 23s_blastdb_dir - 5s_model_path - AntiFamLib - asn2pas_xsl - blast_rules_db_dir - CDDdata2 - CDDdata - defline_cleanup_rules - gene_master_ini - genemark_path - hmm_path - hmms_tab - naming_blast_db - naming_hmms_combined - naming_hmms_tab - naming_sqlite - rfam_amendments - rfam_model_path - rfam_stockholm - selenoproteins - species_genome_size - taxon_db - thresholds - uniColl_cache - univ_prot_xml - val_res_den_xml - wp_hashes genomic_source: # PLANE run: genomic_source/wf_genomic_source_asn.cwl in: entries: entries seq_submit: seq_submit # taxid: taxid gc_assm_name: ping_start/outstring taxon_db: passdata/taxon_db out: [gencoll_asn, seqid_list, stats_report, asncache, ids_out, submit_block_template] # # Pseudo plane "default 1" # Prepare_Unannotated_Sequences: # ORIGINAL TASK NAME: Prepare Unannotated Sequences # default 1 label: "Prepare Unannotated Sequences" run: bacterial_prepare_unannotated.cwl in: asn_cache: genomic_source/asncache gc_assembly: genomic_source/gencoll_asn ids: genomic_source/seqid_list submit_block: genomic_source/submit_block_template taxon_db: passdata/taxon_db out: [master_desc, sequences] Prepare_Unannotated_Sequences_pgapx_input_check: run: progs/pgapx_input_check.cwl in: input: Prepare_Unannotated_Sequences/sequences max_size: { default: 15000000 } min_size: { default: 300 } species_genome_size: passdata/species_genome_size taxon_db: passdata/taxon_db out: [] Prepare_Unannotated_Sequences_text: run: progs/asn_translator.cwl in: input: Prepare_Unannotated_Sequences/sequences output_output: {default: 'sequences.text.asn'} out: [output] Prepare_Unannotated_Sequences_asndisc_cpp: run: progs/asndisc_cpp.cwl in: XML: {default: true} genbank: {default: true} P: {default: 't'} a: {default: 'c'} asn_cache: genomic_source/asncache o_output: {default: 'sequences.disc.xml'} i: Prepare_Unannotated_Sequences_text/output out: [o] Prepare_Unannotated_Sequences_asnvalidate: run: progs/asnvalidate.cwl in: Q: default: 0 R: default: 5 a: default: 'e' i: Prepare_Unannotated_Sequences/sequences o_output: default: 'sequences.val' v: { default: 4 } A: default: true U: default: true Z: default: true b: default: true out: [o] Cache_Entrez_Gene: # ORIGINAL TASK NAME: Cache Entrez Gene # default 1 label: "Cache Entrez Gene" run: cache_entrez_gene.cwl in: asn_cache: [genomic_source/asncache, passdata/uniColl_cache] egene_ini: passdata/gene_master_ini input: Prepare_Unannotated_Sequences/sequences out: [prok_entrez_gene_stuff] Create_Genomic_BLASTdb: # default 1 label: "Create Genomic BLASTdb" # default 1 run: progs/gp_makeblastdb.cwl in: ids: genomic_source/ids_out title: default: 'BLASTdb created by GPipe' asn_cache: source: [ genomic_source/asncache ] linkMerge: merge_flattened dbtype: default: 'nucl' out: [blastdb] # # end of pseudo plane "default 1" # bacterial_ncrna: # PLANE run: bacterial_ncrna/wf_gcmsearch.cwl in: asn_cache: genomic_source/asncache seqids: genomic_source/seqid_list model_path: passdata/rfam_model_path rfam_amendments: passdata/rfam_amendments rfam_stockholm: passdata/rfam_stockholm taxon_db: passdata/taxon_db out: [annots] bacterial_mobile_elem: # PLANE run: bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl in: asn_cache: genomic_source/asncache seqids: genomic_source/seqid_list out: [annots] bacterial_noncoding: # PLANE run: bacterial_noncoding/wf_bacterial_noncoding.cwl in: asn_cache: genomic_source/asncache seqids: genomic_source/seqid_list 16s_blastdb_dir: passdata/16s_blastdb_dir 23s_blastdb_dir: passdata/23s_blastdb_dir model_path: passdata/5s_model_path rfam_amendments: passdata/rfam_amendments rfam_stockholm: passdata/rfam_stockholm taxon_db: passdata/taxon_db out: [ annotations_5s, annotations_16s, annotations_23s ] bacterial_trna: # PLANE run: bacterial_trna/wf_trnascan.cwl in: asn_cache: genomic_source/asncache seqids: genomic_source/seqid_list taxid: taxid taxon_db: passdata/taxon_db scatter_gather_nchunks: scatter_gather_nchunks out: [annots] bacterial_annot: # PLANE run: bacterial_annot/wf_bacterial_annot_pass1.cwl in: asn_cache: genomic_source/asncache inseq: Prepare_Unannotated_Sequences/sequences hmm_path: passdata/hmm_path hmms_tab: passdata/hmms_tab scatter_gather_nchunks: scatter_gather_nchunks uniColl_cache: passdata/uniColl_cache trna_annots: bacterial_trna/annots ncrna_annots: bacterial_ncrna/annots nogenbank: default: true Execute_CRISPRs_annots: bacterial_mobile_elem/annots Generate_16S_rRNA_Annotation_annotation: bacterial_noncoding/annotations_16s Generate_23S_rRNA_Annotation_annotation: bacterial_noncoding/annotations_23s Post_process_CMsearch_annotations_annots_5S: bacterial_noncoding/annotations_5s genemark_path: passdata/genemark_path thresholds: passdata/thresholds out: [lds2,seqids,proteins, aligns, annotation, out_hmm_params, outseqs, prot_ids] spurious_annot_1: # PLANE run: spurious_annot/wf_spurious_annot_pass1.cwl in: Extract_ORF_Proteins_proteins: bacterial_annot/proteins Extract_ORF_Proteins_seqids: bacterial_annot/seqids Extract_ORF_Proteins_lds2: bacterial_annot/lds2 AntiFamLib: passdata/AntiFamLib sequence_cache: genomic_source/asncache scatter_gather_nchunks: scatter_gather_nchunks out: [AntiFam_tainted_proteins_I___oseqids] bacterial_annot_2: # PLANE run: bacterial_annot/wf_bacterial_annot_pass2.cwl in: lds2: bacterial_annot/lds2 proteins: bacterial_annot/proteins prot_ids_A: bacterial_annot/seqids prot_ids_B1: bacterial_annot/prot_ids prot_ids_B2: spurious_annot_1/AntiFam_tainted_proteins_I___oseqids blast_rules_db_dir: passdata/blast_rules_db_dir blast_rules_db: blast_rules_db identification_db_dir: passdata/naming_blast_db annotation: bacterial_annot/outseqs sequence_cache: genomic_source/asncache unicoll_cache: passdata/uniColl_cache scatter_gather_nchunks: scatter_gather_nchunks out: [aligns] # label: "goes to protein_alignment/Seed Search Compartments/compartments" protein_alignment: # PLANE run: protein_alignment/wf_protein_alignment.cwl in: asn_cache: genomic_source/asncache uniColl_asn_cache: passdata/uniColl_cache naming_sqlite: passdata/naming_sqlite blastdb_dir: Create_Genomic_BLASTdb/blastdb taxid: taxid tax_sql_file: passdata/taxon_db gc_assembly: genomic_source/gencoll_asn compartments: bacterial_annot_2/aligns out: [universal_clusters, align, align_non_match] bacterial_annot_3: run: bacterial_annot/wf_bacterial_annot_pass3.cwl in: uniColl_cache: passdata/uniColl_cache sequence_cache: genomic_source/asncache hmm_aligns: bacterial_annot/aligns scatter_gather_nchunks: scatter_gather_nchunks prot_aligns: protein_alignment/align # label: "Filter Protein Alignments I/align" annotation: bacterial_annot/annotation raw_seqs: Prepare_Unannotated_Sequences/sequences thresholds: passdata/thresholds naming_sqlite: passdata/naming_sqlite hmm_params: bacterial_annot/out_hmm_params # Run GeneMark Training/hmm_params (EXTERNAL, put to input/ selenoproteins: passdata/selenoproteins naming_hmms_combined: passdata/naming_hmms_combined hmms_tab: passdata/naming_hmms_tab wp_hashes: passdata/wp_hashes taxon_db: passdata/taxon_db genemark_path: passdata/genemark_path out: - id: Find_Best_Evidence_Alignments_aligns - id: Run_GeneMark_Post_models - id: Extract_Model_Proteins_seqids - id: Extract_Model_Proteins_lds2 - id: Extract_Model_Proteins_proteins - id: Search_Naming_HMMs_hmm_hits - id: Assign_Naming_HMM_to_Proteins_assignments - id: Name_by_WPs_names spurious_annot_2: run: spurious_annot/wf_spurious_annot_pass2.cwl in: Extract_Model_Proteins_proteins: bacterial_annot_3/Extract_Model_Proteins_proteins Extract_Model_Proteins_seqids: bacterial_annot_3/Extract_Model_Proteins_seqids Extract_Model_Proteins_lds2: bacterial_annot_3/Extract_Model_Proteins_lds2 AntiFamLib: passdata/AntiFamLib sequence_cache: genomic_source/asncache scatter_gather_nchunks: scatter_gather_nchunks Run_GeneMark_models: bacterial_annot_3/Run_GeneMark_Post_models out: - AntiFam_tainted_proteins___oseqids - Good_AntiFam_filtered_annotations_out - Good_AntiFam_filtered_proteins_output bacterial_annot_4: run: bacterial_annot/wf_bacterial_annot_pass4.cwl in: lds2: bacterial_annot_3/Extract_Model_Proteins_lds2 proteins: bacterial_annot_3/Extract_Model_Proteins_proteins annotation: spurious_annot_2/Good_AntiFam_filtered_annotations_out Good_AntiFam_filtered_proteins_gilist: spurious_annot_2/Good_AntiFam_filtered_proteins_output sequence_cache: genomic_source/asncache uniColl_cache: passdata/uniColl_cache naming_blast_db: passdata/naming_blast_db naming_sqlite: passdata/naming_sqlite hmm_assignments: bacterial_annot_3/Assign_Naming_HMM_to_Proteins_assignments wp_assignments: bacterial_annot_3/Name_by_WPs_names Extract_Model_Proteins_prot_ids: bacterial_annot_3/Extract_Model_Proteins_seqids CDDdata: passdata/CDDdata CDDdata2: passdata/CDDdata2 thresholds: passdata/thresholds defline_cleanup_rules: passdata/defline_cleanup_rules blast_rules_db_dir: passdata/blast_rules_db_dir blast_rules_db: blast_rules_db identification_db_dir: passdata/naming_blast_db scatter_gather_nchunks: scatter_gather_nchunks out: - id: out_annotation # # # # Pseudo plane default 2, we do not need that for new submissions in off-NCBI environment # # # # Preserve_Annotations: # Pseudo plane default 2 # # run: task_types/tt_preserve_annot.cwl # # in: # # asn_cache: # # source: [genomic_source/asncache] # # linkMerge: merge_flattened # # input_annotation: bacterial_annot/annotation # # rfam_amendments: rfam_amendments # # no_ncRNA: # # default: true # # out: [annotations] # # preserve_annot_markup: # Pseudo plane default 2 # # # uncharted territory!!! # # run: preserve_annot_markup.cwl # Preserve Product Accessions # # in: # # #seq_cache: genobacterial_prepare_unannotated/asncache # # #unicoll_cache: uniColl_cache # # input_annotation: Preserve_Annotations/annotations # # asn_cache: [genomic_source/asncache, uniColl_cache] # # egene_ini: gene_master_ini # # gc_assembly: genomic_source/gencoll_asn # # input: Preserve_Annotations/annotations # # prok_entrez_gene_stuff: Cache_Entrez_Gene/prok_entrez_gene_stuff # # out: [annotations] # # # # End of Pseudo plane default 2 # # # # This step takes input from bacterial_annot 4/Bacterial Annot Filter, see GP-23942 # # Status: # # tasktype coded, input/output matches # # application not coded # ############################################### # # AMR plane is for later stages skipping # ############################################### Add_Locus_Tags: run: progs/add_locus_tags.cwl in: input: bacterial_annot_4/out_annotation locus_tag_prefix: locus_tag_prefix dbname: dbname out: [output] # # Pseudo plane default 3 # # # Final_Bacterial_Package task # Final_Bacterial_Package_asn_cleanup: run: progs/asn_cleanup.cwl in: inp_annotation: Add_Locus_Tags/output # production serial: default: binary out: [annotation] Final_Bacterial_Package_final_bact_asn: run: progs/final_bact_asn.cwl in: annotation: source: [Final_Bacterial_Package_asn_cleanup/annotation] linkMerge: merge_flattened asn_cache: genomic_source/asncache gc_assembly: genomic_source/gencoll_asn # gc_create_from_sequences master_desc: Prepare_Unannotated_Sequences/master_desc it: default: true submission_mode_genbank: default: true nogenbank: default: true out: [outfull] Final_Bacterial_Package_dumb_down_as_required: run: progs/dumb_down_as_required.cwl in: annotation: Final_Bacterial_Package_final_bact_asn/outfull asn_cache: source: [genomic_source/asncache] linkMerge: merge_flattened max_x_ratio: default: 0.1 max_x_run: default: 3 partial_cov_threshold: default: 65 partial_len_threshold: default: 30 drop_partial_in_the_middle: default: true submission_mode_genbank: default: true submol_block_json: submol_block_json nogenbank: default: true it: default: true out: [outent] Final_Bacterial_Package_ent2sqn: run: progs/ent2sqn.cwl in: annotation: Final_Bacterial_Package_dumb_down_as_required/outent asn_cache: source: [genomic_source/asncache] linkMerge: merge_flattened gc_assembly: genomic_source/gencoll_asn # gc_create_from_sequences submit_block_template: source: [genomic_source/submit_block_template] linkMerge: merge_flattened it: default: true output_impl: default: annot-wo-checksum.sqn out: [output] add_checksum_sqn: label: Add Checksum to SQN run: progs/annot_checksum.cwl in: input: Final_Bacterial_Package_ent2sqn/output output_name: default: 'annot.sqn' t: default: true ifmt: default: seq-submit mode: default: add out: [output] Final_Bacterial_Package_sqn2gbent: run: progs/sqn2gbent.cwl doc: We are not taking here sqn with added annot checksum. in: input: Final_Bacterial_Package_ent2sqn/output it: default: true out_name: default: annot-gb-wo-checksum.ent out: [output] add_checksum_gbent: label: Add Checksum to Genbank class ENT run: progs/annot_checksum.cwl in: input: Final_Bacterial_Package_sqn2gbent/output output_name: default: 'annot-gb.ent' t: default: true ifmt: default: seq-entry mode: default: add out: [output] Generate_Annotation_Reports_gff: run: progs/gp_annot_format.cwl in: input: Final_Bacterial_Package_dumb_down_as_required/outent ifmt: default: seq-entry t: default: true ofmt: default: gff3 exclude_external: default: true out: [output] Generate_Annotation_Reports_gbk: run: progs/asn2flat.cwl in: input: Final_Bacterial_Package_sqn2gbent/output no_external: default: true type: default: seq-entry mode: default: entrez style: default: master gbload: default: true out: [output] Generate_Annotation_Reports_nuc_fasta: run: progs/asn2fasta.cwl in: i: Final_Bacterial_Package_sqn2gbent/output type: default: seq-entry nuc_fasta_name: default: annot.fna out: [nuc_fasta] Generate_Annotation_Reports_prot_fasta: run: progs/asn2fasta.cwl in: i: Final_Bacterial_Package_sqn2gbent/output type: default: seq-entry prot_fasta_name: default: annot.faa out: [prot_fasta] Final_Bacterial_Package_std_validation: run: progs/std_validation.cwl in: annotation: Final_Bacterial_Package_dumb_down_as_required/outent asn_cache: source: [genomic_source/asncache] exclude_asndisc_codes: # default: ['OVERLAPPING_CDS'] inent: Final_Bacterial_Package_dumb_down_as_required/outent ingb: Final_Bacterial_Package_sqn2gbent/output insqn: Final_Bacterial_Package_ent2sqn/output master_desc: source: [Prepare_Unannotated_Sequences/master_desc] linkMerge: merge_flattened submit_block_template: source: [genomic_source/submit_block_template] linkMerge: merge_flattened it: default: true submission_mode_genbank: default: true nogenbank: default: true out: - id: outdisc - id: outdiscxml - id: outmetamaster - id: outval Final_Bacterial_Package_val_stats: # TESTED (unit test) run: progs/val_stats.cwl in: annot_val: Final_Bacterial_Package_std_validation/outval c_toolkit: default: true out: [output, xml] # # end of Final_Bacterial_Package task # #### we do not need this # Prepare_Init_Refseq_Molecules: # run: progs/ # # Validate_Annotation task # Validate_Annotation_bact_univ_prot_stats: run: progs/bact_univ_prot_stats.cwl in: annot_request_id: default: -1 # this is dummy annot_request_id hmm_search: bacterial_annot_3/Search_Naming_HMMs_hmm_hits hmm_search_proteins: bacterial_annot_3/Run_GeneMark_Post_models input: Final_Bacterial_Package_final_bact_asn/outfull univ_prot_xml: passdata/univ_prot_xml val_res_den_xml: passdata/val_res_den_xml it: default: true out: [bact_univ_prot_stats_old_xml, var_bact_univ_prot_details_xml, var_bact_univ_prot_stats_xml] Validate_Annotation_proc_annot_stats: run: progs/proc_annot_stats.cwl in: input: Final_Bacterial_Package_dumb_down_as_required/outent max_unannotated_region: default: 5000 univ_prot_xml: passdata/univ_prot_xml val_res_den_xml: passdata/val_res_den_xml it: default: true out: - id: var_proc_annot_stats_xml - id: var_proc_annot_details_xml Validate_Annotation_xsltproc_asnvalidate: run: progs/xsltproc.cwl in: xml: Final_Bacterial_Package_val_stats/xml xslt: passdata/asn2pas_xsl output_name: default: 'var_proc_annot_stats.val.xml' out: [output] Validate_Annotation_xsltproc_asndisc: run: progs/xsltproc.cwl in: xml: Final_Bacterial_Package_std_validation/outdiscxml xslt: passdata/asn2pas_xsl output_name: default: 'var_proc_annot_stats.disc.xml' out: [output] Validate_Annotation_collect_annot_stats: # TESTED (unit test) run: progs/collect_annot_stats.cwl in: input: source: - Validate_Annotation_bact_univ_prot_stats/var_bact_univ_prot_stats_xml - Validate_Annotation_proc_annot_stats/var_proc_annot_stats_xml - Validate_Annotation_xsltproc_asndisc/output - Validate_Annotation_xsltproc_asnvalidate/output linkMerge: merge_flattened output_name: default: proc_annot_stats.xml out: [output] Validate_Annotation_collect_annot_details: run: progs/collect_annot_stats.cwl in: input: source: - Validate_Annotation_bact_univ_prot_stats/var_bact_univ_prot_details_xml - Validate_Annotation_proc_annot_stats/var_proc_annot_details_xml linkMerge: merge_flattened output_name: default: proc_annot_details.xml out: [output] ping_stop: run: progs/pinger.cwl in: report_usage: report_usage uuid_in: ping_start/uuid_out state: default: "stop" workflow: default: "pgap" # Note: the input on the following line should be the same as all of the outputs # for this workflow, so we ensure this is the final step. infile: - Final_Bacterial_Package_sqn2gbent/output - Generate_Annotation_Reports_gff/output - Generate_Annotation_Reports_gbk/output - Generate_Annotation_Reports_nuc_fasta/nuc_fasta - Generate_Annotation_Reports_prot_fasta/prot_fasta out: [stdout] # # end of Validate_Annotation task # # # End of Pseudo plane default 3 # ############################################### # taxonomy plane is for later stages skipping ############################################### # # Pseudo plane default 4 # # task: Generate Annotation Reports # # Generate_Annotation_Reports_pgaap_prepare_review: # run: progs/pgaap_prepare_review.cwl # Generate_Annotation_Reports_lds2_indexer: # run: progs/lds2_indexer.cwl # # comparisons only for pre-existing annotation, one of the next phases # # # Generate_Annotation_Reports_comparison_format_curr_comparison: # # run: progs/comparison_format.cwl # # Generate_Annotation_Reports_comparison_format_prev_comparison: # # run: progs/comparison_format.cwl # # Generate_Annotation_Reports_comparison_format_prev_assm_comparison: # # run: progs/comparison_format.cwl # # Generate_Annotation_Reports_comparison_format_ref_comparison: # # run: progs/comparison_format.cwl # Generate_Annotation_Reports_bact_asn_stats: # run: progs/bact_asn_stats.cwl # in: # input_annotation: Final_Bacterial_Package_dumb_down_as_required/outent # it: # default: true # out: [output, xml_output] # Generate_Annotation_Reports_val_format: # run: progs/val_format.cwl # Generate_Annotation_Reports_gbproject: # run: progs/gbproject.cwl # Generate_Annotation_Reports_asn2nucleotide_fasta: # run: progs/asn2fasta.cwl # Generate_Annotation_Reports_asn2all_protein_fasta: # run: progs/asn2fasta.cwl # Generate_Annotation_Reports_asn2protein_fasta: # run: progs/asn2fasta.cwl # Generate_Annotation_Reports_asn2flat: # run: progs/asn2flat.cwl # Generate_Annotation_Reports_format_rrnas: # run: progs/format_rrnas.cwl # Generate_Annotation_Reports_asn2rrna_fa: # run: progs/asn2fasta.cwl # Generate_Annotation_Reports_gp_annot_format: # run: progs/gp_annot_format.cwl # end of task: Generate Annotation Reports # # # End of Pseudo plane default 4 # outputs: gbent: type: File outputSource: add_checksum_gbent/output gff: type: File outputSource: Generate_Annotation_Reports_gff/output gbk: type: File outputSource: Generate_Annotation_Reports_gbk/output nucleotide_fasta: type: File? outputSource: Generate_Annotation_Reports_nuc_fasta/nuc_fasta protein_fasta: type: File? outputSource: Generate_Annotation_Reports_prot_fasta/prot_fasta sqn: type: File outputSource: add_checksum_sqn/output