From 0f31c49174408cae6637fca528a4b37ed5446a19 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 17 Jul 2024 15:31:15 +0000 Subject: [PATCH 1/4] optionalize characterization with new boolean input --- workflows/theiaprok/wf_theiaprok_fasta.wdl | 755 +++++++-------- .../theiaprok/wf_theiaprok_illumina_pe.wdl | 869 +++++++++--------- .../theiaprok/wf_theiaprok_illumina_se.wdl | 803 ++++++++-------- workflows/theiaprok/wf_theiaprok_ont.wdl | 790 ++++++++-------- 4 files changed, 1615 insertions(+), 1602 deletions(-) diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index 0176eb955..9c5fb4498 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -36,6 +36,7 @@ workflow theiaprok_fasta { String terra_project="NA" String terra_workspace="NA" # module options + Boolean perform_characterization = true # by default run all characterization steps Boolean call_ani = false # by default do not call ANI task, but user has ability to enable this task if working with enteric pathogens or supply their own high-quality reference genome Boolean call_kmerfinder = false Boolean call_resfinder = false @@ -59,386 +60,388 @@ workflow theiaprok_fasta { input: assembly = assembly_fasta, samplename = samplename - } + } call busco_task.busco { input: assembly = assembly_fasta, samplename = samplename } - if (call_ani) { - call ani_task.animummer as ani { - input: - assembly = assembly_fasta, - samplename = samplename + if (perform_characterization) { + if (call_ani) { + call ani_task.animummer as ani { + input: + assembly = assembly_fasta, + samplename = samplename + } } - } - if (call_kmerfinder) { - call kmerfinder_task.kmerfinder_bacteria as kmerfinder { - input: - assembly = assembly_fasta, - samplename = samplename + if (call_kmerfinder) { + call kmerfinder_task.kmerfinder_bacteria as kmerfinder { + input: + assembly = assembly_fasta, + samplename = samplename + } } - } - call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { - input: - assembly = assembly_fasta, - samplename = samplename, - organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) - } - if (call_resfinder) { - call resfinder.resfinder as resfinder_task { + call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { input: assembly = assembly_fasta, samplename = samplename, organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) } - } - call ts_mlst_task.ts_mlst { - input: - assembly = assembly_fasta, - samplename = samplename - } - if (genome_annotation == "prokka") { - call prokka_task.prokka { - input: - assembly = assembly_fasta, - samplename = samplename + if (call_resfinder) { + call resfinder.resfinder as resfinder_task { + input: + assembly = assembly_fasta, + samplename = samplename, + organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) + } } - } - if (genome_annotation == "bakta") { - call bakta_task.bakta { - input: + call ts_mlst_task.ts_mlst { + input: assembly = assembly_fasta, samplename = samplename } - } - if (call_plasmidfinder) { - call plasmidfinder_task.plasmidfinder { - input: - assembly = assembly_fasta, - samplename = samplename + if (genome_annotation == "prokka") { + call prokka_task.prokka { + input: + assembly = assembly_fasta, + samplename = samplename + } } - } - if (call_abricate) { - call abricate_task.abricate { + if (genome_annotation == "bakta") { + call bakta_task.bakta { + input: + assembly = assembly_fasta, + samplename = samplename + } + } + if (call_plasmidfinder) { + call plasmidfinder_task.plasmidfinder { + input: + assembly = assembly_fasta, + samplename = samplename + } + } + if (call_abricate) { + call abricate_task.abricate { + input: + assembly = assembly_fasta, + samplename = samplename, + database = abricate_db + } + } + call merlin_magic_workflow.merlin_magic { input: + merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), assembly = assembly_fasta, samplename = samplename, - database = abricate_db + assembly_only = true, + paired_end = false } - } - call merlin_magic_workflow.merlin_magic { - input: - merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), - assembly = assembly_fasta, - samplename = samplename, - assembly_only = true, - paired_end = false - } - if (defined(qc_check_table)) { - call qc_check.qc_check_phb as qc_check_task { - input: - qc_check_table = qc_check_table, - expected_taxon = expected_taxon, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - busco_results = busco.busco_results, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + if (defined(qc_check_table)) { + call qc_check.qc_check_phb as qc_check_task { + input: + qc_check_table = qc_check_table, + expected_taxon = expected_taxon, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + busco_results = busco.busco_results, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + } } - } - if (defined(taxon_tables)) { - call terra_tools.export_taxon_tables { - input: - terra_project = terra_project, - terra_workspace = terra_workspace, - sample_taxon = gambit.gambit_predicted_taxon, - taxon_tables = taxon_tables, - samplename = samplename, - run_id = run_id, - collection_date = collection_date, - originating_lab = originating_lab, - city = city, - county = county, - zip = zip, - theiaprok_fasta_version = version_capture.phb_version, - theiaprok_fasta_analysis_date = version_capture.date, - seq_platform = seq_method, - quast_report = quast.quast_report, - quast_version = quast.version, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - gambit_report = gambit.gambit_report_file, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, - gambit_closest_genomes = gambit.gambit_closest_genomes_file, - gambit_version = gambit.gambit_version, - gambit_db_version = gambit.gambit_db_version, - gambit_docker = gambit.gambit_docker, - busco_version = busco.busco_version, - busco_database = busco.busco_database, - busco_results = busco.busco_results, - busco_report = busco.busco_report, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, - ani_output_tsv = ani.ani_output_tsv, - ani_top_species_match = ani.ani_top_species_match, - ani_mummer_version = ani.ani_mummer_version, - ani_docker = ani.ani_docker, - kmerfinder_docker = kmerfinder.kmerfinder_docker, - kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, - kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, - kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, - kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, - kmerfinder_database = kmerfinder.kmerfinder_database, - amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, - amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, - amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, - amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, - amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, - amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, - amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, - amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, - amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, - amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, - amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, - amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, - resfinder_pheno_table = resfinder_task.resfinder_pheno_table, - resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, - resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, - resfinder_results = resfinder_task.resfinder_results_tab, - resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, - resfinder_pointfinder_results = resfinder_task.pointfinder_results, - resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, - resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, - resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, - resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, - resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, - resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, - resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, - resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, - resfinder_db_version = resfinder_task.resfinder_db_version, - resfinder_docker = resfinder_task.resfinder_docker, - ts_mlst_results = ts_mlst.ts_mlst_results, - ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, - ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, - ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, - ts_mlst_version = ts_mlst.ts_mlst_version, - ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, - ts_mlst_docker = ts_mlst.ts_mlst_docker, - serotypefinder_report = merlin_magic.serotypefinder_report, - serotypefinder_docker = merlin_magic.serotypefinder_docker, - serotypefinder_serotype = merlin_magic.serotypefinder_serotype, - ectyper_results = merlin_magic.ectyper_results, - ectyper_version = merlin_magic.ectyper_version, - ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, - shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, - shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, - shigatyper_notes = merlin_magic.shigatyper_notes, - shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, - shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, - shigatyper_version = merlin_magic.shigatyper_version, - shigatyper_docker = merlin_magic.shigatyper_docker, - shigeifinder_report = merlin_magic.shigeifinder_report, - shigeifinder_docker = merlin_magic.shigeifinder_docker, - shigeifinder_version = merlin_magic.shigeifinder_version, - shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, - shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, - shigeifinder_cluster = merlin_magic.shigeifinder_cluster, - shigeifinder_serotype = merlin_magic.shigeifinder_serotype, - shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, - shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, - shigeifinder_notes = merlin_magic.shigeifinder_notes, - shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, - shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, - shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, - shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, - shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, - shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, - shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, - shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, - shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, - shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, - virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, - virulencefinder_docker = merlin_magic.virulencefinder_docker, - virulencefinder_hits = merlin_magic.virulencefinder_hits, - sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, - sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, - sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, - sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, - sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, - sonneityping_species = merlin_magic.sonneityping_species, - sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, - sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, - sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, - lissero_results = merlin_magic.lissero_results, - lissero_version = merlin_magic.lissero_version, - lissero_serotype = merlin_magic.lissero_serotype, - sistr_results = merlin_magic.sistr_results, - sistr_allele_json = merlin_magic.sistr_allele_json, - sistr_allele_fasta = merlin_magic.sistr_allele_fasta, - sistr_cgmlst = merlin_magic.sistr_cgmlst, - sistr_version = merlin_magic.sistr_version, - sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, - seqsero2_report = merlin_magic.seqsero2_report, - seqsero2_version = merlin_magic.seqsero2_version, - seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, - seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, - seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, - genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, - genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, - genotyphi_version = merlin_magic.genotyphi_version, - genotyphi_species = merlin_magic.genotyphi_species, - genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, - genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, - genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, - kleborate_output_file = merlin_magic.kleborate_output_file, - kleborate_version = merlin_magic.kleborate_version, - kleborate_docker = merlin_magic.kleborate_docker, - kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, - kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, - kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, - kleborate_klocus = merlin_magic.kleborate_klocus, - kleborate_ktype = merlin_magic.kleborate_ktype, - kleborate_olocus = merlin_magic.kleborate_olocus, - kleborate_otype = merlin_magic.kleborate_otype, - kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, - kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, - kleborate_virulence_score = merlin_magic.kleborate_virulence_score, - kleborate_resistance_score = merlin_magic.kleborate_resistance_score, - ngmaster_tsv = merlin_magic.ngmaster_tsv, - ngmaster_version = merlin_magic.ngmaster_version, - ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, - ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, - ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, - ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, - ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, - ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, - ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, - ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, - ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, - ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, - ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, - meningotype_tsv = merlin_magic.meningotype_tsv, - meningotype_version = merlin_magic.meningotype_version, - meningotype_serogroup = merlin_magic.meningotype_serogroup, - meningotype_PorA = merlin_magic.meningotype_PorA, - meningotype_FetA = merlin_magic.meningotype_FetA, - meningotype_PorB = merlin_magic.meningotype_PorB, - meningotype_fHbp = merlin_magic.meningotype_fHbp, - meningotype_NHBA = merlin_magic.meningotype_NHBA, - meningotype_NadA = merlin_magic.meningotype_NadA, - meningotype_BAST = merlin_magic.meningotype_BAST, - kaptive_output_file_k = merlin_magic.kaptive_output_file_k, - kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, - kaptive_version = merlin_magic.kaptive_version, - kaptive_k_locus = merlin_magic.kaptive_k_match, - kaptive_k_type = merlin_magic.kaptive_k_type, - kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, - kaptive_oc_locus = merlin_magic.kaptive_oc_match, - kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, - abricate_results_tsv = abricate.abricate_results, - abricate_genes = abricate.abricate_genes, - abricate_database = abricate.abricate_database, - abricate_version = abricate.abricate_version, - abricate_docker = abricate.abricate_docker, - abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, - abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, - abricate_abaum_database = merlin_magic.abricate_abaum_database, - abricate_abaum_version = merlin_magic.abricate_abaum_version, - abricate_abaum_docker = merlin_magic.abricate_abaum_docker, - tbprofiler_output_file = merlin_magic.tbprofiler_output_file, - tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, - tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, - tbprofiler_version = merlin_magic.tbprofiler_version, - tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, - tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, - tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, - tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, - legsta_results = merlin_magic.legsta_results, - legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, - legsta_version = merlin_magic.legsta_version, - prokka_gff = prokka.prokka_gff, - prokka_gbk = prokka.prokka_gbk, - prokka_sqn = prokka.prokka_sqn, - bakta_gbff = bakta.bakta_gbff, - bakta_gff3 = bakta.bakta_gff3, - bakta_tsv = bakta.bakta_tsv, - bakta_summary = bakta.bakta_txt, - bakta_version = bakta.bakta_version, - plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, - plasmidfinder_results = plasmidfinder.plasmidfinder_results, - plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, - plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, - plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, - pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, - pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, - pbptyper_version = merlin_magic.pbptyper_version, - pbptyper_docker = merlin_magic.pbptyper_docker, - poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, - poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, - poppunk_GPS_db_version = merlin_magic.poppunk_gps_external_cluster_csv, - poppunk_version = merlin_magic.poppunk_version, - poppunk_docker = merlin_magic.poppunk_docker, - spatyper_tsv = merlin_magic.spatyper_tsv, - spatyper_docker = merlin_magic.spatyper_docker, - spatyper_repeats = merlin_magic.spatyper_repeats, - spatyper_type = merlin_magic.spatyper_type, - spatyper_version = merlin_magic.spatyper_version, - staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, - staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, - staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, - staphopiasccmec_version = merlin_magic.staphopiasccmec_version, - staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, - agrvate_summary = merlin_magic.agrvate_summary, - agrvate_results = merlin_magic.agrvate_results, - agrvate_agr_group = merlin_magic.agrvate_agr_group, - agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, - agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, - agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, - agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, - agrvate_version = merlin_magic.agrvate_version, - agrvate_docker = merlin_magic.agrvate_docker, - seroba_version = merlin_magic.seroba_version, - seroba_docker = merlin_magic.seroba_docker, - seroba_serotype = merlin_magic.seroba_serotype, - seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype, - seroba_ariba_identity = merlin_magic.seroba_ariba_identity, - seroba_details = merlin_magic.seroba_details, - emmtyper_emm_type = merlin_magic.emmtyper_emm_type, - emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, - emmtyper_version = merlin_magic.emmtyper_version, - emmtyper_docker = merlin_magic.emmtyper_docker, - pasty_serogroup = merlin_magic.pasty_serogroup, - pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, - pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, - pasty_summary_tsv = merlin_magic.pasty_summary_tsv, - pasty_blast_hits = merlin_magic.pasty_blast_hits, - pasty_all_serogroups = merlin_magic.pasty_all_serogroups, - pasty_version = merlin_magic.pasty_version, - pasty_docker = merlin_magic.pasty_docker, - pasty_comment = merlin_magic.pasty_comment, - qc_check = qc_check_task.qc_check, - qc_standard = qc_check_task.qc_standard, - hicap_serotype = merlin_magic.hicap_serotype, - hicap_genes = merlin_magic.hicap_genes, - hicap_results_tsv = merlin_magic.hicap_results_tsv, - hicap_version = merlin_magic.hicap_version, - hicap_docker = merlin_magic.hicap_docker, - abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, - abricate_vibrio_database = merlin_magic.abricate_vibrio_database, - abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, - abricate_vibrio_version = merlin_magic.abricate_vibrio_version, - abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, - abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, - abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, - abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, - abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + if (defined(taxon_tables)) { + call terra_tools.export_taxon_tables { + input: + terra_project = terra_project, + terra_workspace = terra_workspace, + sample_taxon = gambit.gambit_predicted_taxon, + taxon_tables = taxon_tables, + samplename = samplename, + run_id = run_id, + collection_date = collection_date, + originating_lab = originating_lab, + city = city, + county = county, + zip = zip, + theiaprok_fasta_version = version_capture.phb_version, + theiaprok_fasta_analysis_date = version_capture.date, + seq_platform = seq_method, + quast_report = quast.quast_report, + quast_version = quast.version, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + gambit_report = gambit.gambit_report_file, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, + gambit_closest_genomes = gambit.gambit_closest_genomes_file, + gambit_version = gambit.gambit_version, + gambit_db_version = gambit.gambit_db_version, + gambit_docker = gambit.gambit_docker, + busco_version = busco.busco_version, + busco_database = busco.busco_database, + busco_results = busco.busco_results, + busco_report = busco.busco_report, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, + ani_output_tsv = ani.ani_output_tsv, + ani_top_species_match = ani.ani_top_species_match, + ani_mummer_version = ani.ani_mummer_version, + ani_docker = ani.ani_docker, + kmerfinder_docker = kmerfinder.kmerfinder_docker, + kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, + kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, + kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, + kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, + kmerfinder_database = kmerfinder.kmerfinder_database, + amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, + amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, + amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, + amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, + amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, + amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, + amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, + amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, + amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, + amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, + amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, + amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, + resfinder_pheno_table = resfinder_task.resfinder_pheno_table, + resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, + resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, + resfinder_results = resfinder_task.resfinder_results_tab, + resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, + resfinder_pointfinder_results = resfinder_task.pointfinder_results, + resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, + resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, + resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, + resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, + resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, + resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, + resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, + resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, + resfinder_db_version = resfinder_task.resfinder_db_version, + resfinder_docker = resfinder_task.resfinder_docker, + ts_mlst_results = ts_mlst.ts_mlst_results, + ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, + ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, + ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, + ts_mlst_version = ts_mlst.ts_mlst_version, + ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, + ts_mlst_docker = ts_mlst.ts_mlst_docker, + serotypefinder_report = merlin_magic.serotypefinder_report, + serotypefinder_docker = merlin_magic.serotypefinder_docker, + serotypefinder_serotype = merlin_magic.serotypefinder_serotype, + ectyper_results = merlin_magic.ectyper_results, + ectyper_version = merlin_magic.ectyper_version, + ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, + shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, + shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, + shigatyper_notes = merlin_magic.shigatyper_notes, + shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, + shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, + shigatyper_version = merlin_magic.shigatyper_version, + shigatyper_docker = merlin_magic.shigatyper_docker, + shigeifinder_report = merlin_magic.shigeifinder_report, + shigeifinder_docker = merlin_magic.shigeifinder_docker, + shigeifinder_version = merlin_magic.shigeifinder_version, + shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, + shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, + shigeifinder_cluster = merlin_magic.shigeifinder_cluster, + shigeifinder_serotype = merlin_magic.shigeifinder_serotype, + shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, + shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, + shigeifinder_notes = merlin_magic.shigeifinder_notes, + shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, + shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, + shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, + shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, + shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, + shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, + shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, + shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, + shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, + shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, + virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, + virulencefinder_docker = merlin_magic.virulencefinder_docker, + virulencefinder_hits = merlin_magic.virulencefinder_hits, + sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, + sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, + sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, + sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, + sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, + sonneityping_species = merlin_magic.sonneityping_species, + sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, + sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, + sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, + lissero_results = merlin_magic.lissero_results, + lissero_version = merlin_magic.lissero_version, + lissero_serotype = merlin_magic.lissero_serotype, + sistr_results = merlin_magic.sistr_results, + sistr_allele_json = merlin_magic.sistr_allele_json, + sistr_allele_fasta = merlin_magic.sistr_allele_fasta, + sistr_cgmlst = merlin_magic.sistr_cgmlst, + sistr_version = merlin_magic.sistr_version, + sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, + seqsero2_report = merlin_magic.seqsero2_report, + seqsero2_version = merlin_magic.seqsero2_version, + seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, + seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, + seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, + genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, + genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, + genotyphi_version = merlin_magic.genotyphi_version, + genotyphi_species = merlin_magic.genotyphi_species, + genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, + genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, + genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, + kleborate_output_file = merlin_magic.kleborate_output_file, + kleborate_version = merlin_magic.kleborate_version, + kleborate_docker = merlin_magic.kleborate_docker, + kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, + kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, + kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, + kleborate_klocus = merlin_magic.kleborate_klocus, + kleborate_ktype = merlin_magic.kleborate_ktype, + kleborate_olocus = merlin_magic.kleborate_olocus, + kleborate_otype = merlin_magic.kleborate_otype, + kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, + kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, + ngmaster_tsv = merlin_magic.ngmaster_tsv, + ngmaster_version = merlin_magic.ngmaster_version, + ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, + ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, + ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, + ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, + ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, + ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, + ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, + ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, + ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, + ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, + ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, + meningotype_tsv = merlin_magic.meningotype_tsv, + meningotype_version = merlin_magic.meningotype_version, + meningotype_serogroup = merlin_magic.meningotype_serogroup, + meningotype_PorA = merlin_magic.meningotype_PorA, + meningotype_FetA = merlin_magic.meningotype_FetA, + meningotype_PorB = merlin_magic.meningotype_PorB, + meningotype_fHbp = merlin_magic.meningotype_fHbp, + meningotype_NHBA = merlin_magic.meningotype_NHBA, + meningotype_NadA = merlin_magic.meningotype_NadA, + meningotype_BAST = merlin_magic.meningotype_BAST, + kaptive_output_file_k = merlin_magic.kaptive_output_file_k, + kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, + kaptive_version = merlin_magic.kaptive_version, + kaptive_k_locus = merlin_magic.kaptive_k_match, + kaptive_k_type = merlin_magic.kaptive_k_type, + kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, + kaptive_oc_locus = merlin_magic.kaptive_oc_match, + kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, + abricate_results_tsv = abricate.abricate_results, + abricate_genes = abricate.abricate_genes, + abricate_database = abricate.abricate_database, + abricate_version = abricate.abricate_version, + abricate_docker = abricate.abricate_docker, + abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, + abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, + abricate_abaum_database = merlin_magic.abricate_abaum_database, + abricate_abaum_version = merlin_magic.abricate_abaum_version, + abricate_abaum_docker = merlin_magic.abricate_abaum_docker, + tbprofiler_output_file = merlin_magic.tbprofiler_output_file, + tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, + tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, + tbprofiler_version = merlin_magic.tbprofiler_version, + tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, + tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, + tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, + tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, + legsta_results = merlin_magic.legsta_results, + legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, + legsta_version = merlin_magic.legsta_version, + prokka_gff = prokka.prokka_gff, + prokka_gbk = prokka.prokka_gbk, + prokka_sqn = prokka.prokka_sqn, + bakta_gbff = bakta.bakta_gbff, + bakta_gff3 = bakta.bakta_gff3, + bakta_tsv = bakta.bakta_tsv, + bakta_summary = bakta.bakta_txt, + bakta_version = bakta.bakta_version, + plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, + plasmidfinder_results = plasmidfinder.plasmidfinder_results, + plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, + plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, + plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, + pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, + pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, + pbptyper_version = merlin_magic.pbptyper_version, + pbptyper_docker = merlin_magic.pbptyper_docker, + poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, + poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, + poppunk_GPS_db_version = merlin_magic.poppunk_gps_external_cluster_csv, + poppunk_version = merlin_magic.poppunk_version, + poppunk_docker = merlin_magic.poppunk_docker, + spatyper_tsv = merlin_magic.spatyper_tsv, + spatyper_docker = merlin_magic.spatyper_docker, + spatyper_repeats = merlin_magic.spatyper_repeats, + spatyper_type = merlin_magic.spatyper_type, + spatyper_version = merlin_magic.spatyper_version, + staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, + staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, + staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, + staphopiasccmec_version = merlin_magic.staphopiasccmec_version, + staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, + agrvate_summary = merlin_magic.agrvate_summary, + agrvate_results = merlin_magic.agrvate_results, + agrvate_agr_group = merlin_magic.agrvate_agr_group, + agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, + agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, + agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, + agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, + agrvate_version = merlin_magic.agrvate_version, + agrvate_docker = merlin_magic.agrvate_docker, + seroba_version = merlin_magic.seroba_version, + seroba_docker = merlin_magic.seroba_docker, + seroba_serotype = merlin_magic.seroba_serotype, + seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype, + seroba_ariba_identity = merlin_magic.seroba_ariba_identity, + seroba_details = merlin_magic.seroba_details, + emmtyper_emm_type = merlin_magic.emmtyper_emm_type, + emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, + emmtyper_version = merlin_magic.emmtyper_version, + emmtyper_docker = merlin_magic.emmtyper_docker, + pasty_serogroup = merlin_magic.pasty_serogroup, + pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, + pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, + pasty_summary_tsv = merlin_magic.pasty_summary_tsv, + pasty_blast_hits = merlin_magic.pasty_blast_hits, + pasty_all_serogroups = merlin_magic.pasty_all_serogroups, + pasty_version = merlin_magic.pasty_version, + pasty_docker = merlin_magic.pasty_docker, + pasty_comment = merlin_magic.pasty_comment, + qc_check = qc_check_task.qc_check, + qc_standard = qc_check_task.qc_standard, + hicap_serotype = merlin_magic.hicap_serotype, + hicap_genes = merlin_magic.hicap_genes, + hicap_results_tsv = merlin_magic.hicap_results_tsv, + hicap_version = merlin_magic.hicap_version, + hicap_docker = merlin_magic.hicap_docker, + abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, + abricate_vibrio_database = merlin_magic.abricate_vibrio_database, + abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, + abricate_vibrio_version = merlin_magic.abricate_vibrio_version, + abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, + abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, + abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, + abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, + abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + } } } output { @@ -483,18 +486,18 @@ workflow theiaprok_fasta { String? kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage String? kmerfinder_database = kmerfinder.kmerfinder_database # NCBI-AMRFinderPlus Outputs - File amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report - File amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report - File amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report - File amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report - String amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes - String amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes - String amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes - String amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes - String amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes - String amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses - String amrfinderplus_version = amrfinderplus_task.amrfinderplus_version - String amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version + File? amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report + File? amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report + File? amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report + File? amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report + String? amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes + String? amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes + String? amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes + String? amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes + String? amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes + String? amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses + String? amrfinderplus_version = amrfinderplus_task.amrfinderplus_version + String? amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version # NCBI-AMRFinderPlus Outputs for BETA-LACTAM genes String? amrfinderplus_amr_betalactam_genes = amrfinderplus_task.amrfinderplus_amr_betalactam_genes String? amrfinderplus_amr_betalactam_betalactam_genes = amrfinderplus_task.amrfinderplus_amr_betalactam_betalactam_genes @@ -520,13 +523,13 @@ workflow theiaprok_fasta { String? resfinder_db_version = resfinder_task.resfinder_db_version String? resfinder_docker = resfinder_task.resfinder_docker # MLST Typing - File ts_mlst_results = ts_mlst.ts_mlst_results - String ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st - String ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme - String ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile - String ts_mlst_version = ts_mlst.ts_mlst_version + File? ts_mlst_results = ts_mlst.ts_mlst_results + String? ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st + String? ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme + String? ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile + String? ts_mlst_version = ts_mlst.ts_mlst_version File? ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles - String ts_mlst_docker = ts_mlst.ts_mlst_docker + String? ts_mlst_docker = ts_mlst.ts_mlst_docker # Prokka Results File? prokka_gff = prokka.prokka_gff File? prokka_gbk = prokka.prokka_gbk diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl index 5906f7cdf..79aa30564 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl @@ -54,6 +54,7 @@ workflow theiaprok_illumina_pe { Int trim_quality_min_score = 20 Int trim_window_size = 10 # module options + Boolean perform_characterization = true # by default run all characterization steps Boolean call_ani = false # by default do not call ANI task, but user has ability to enable this task if working with enteric pathogens or supply their own high-quality reference genome Boolean call_kmerfinder = false Boolean call_resfinder = false @@ -142,455 +143,457 @@ workflow theiaprok_illumina_pe { assembly = shovill_pe.assembly_fasta, samplename = samplename } - if (call_ani) { - call ani_task.animummer as ani { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename + if (perform_characterization) { + if (call_ani) { + call ani_task.animummer as ani { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } } - } - if (call_kmerfinder) { - call kmerfinder_task.kmerfinder_bacteria as kmerfinder { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename + if (call_kmerfinder) { + call kmerfinder_task.kmerfinder_bacteria as kmerfinder { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } } - } - call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename, - organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) - } - if (call_resfinder) { - call resfinder.resfinder as resfinder_task { + call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { input: assembly = shovill_pe.assembly_fasta, samplename = samplename, organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) } - } - call ts_mlst_task.ts_mlst { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename - } - if (genome_annotation == "prokka") { - call prokka_task.prokka { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename + if (call_resfinder) { + call resfinder.resfinder as resfinder_task { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename, + organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) + } } - } - if (genome_annotation == "bakta") { - call bakta_task.bakta { - input: + call ts_mlst_task.ts_mlst { + input: assembly = shovill_pe.assembly_fasta, samplename = samplename } - } - if (call_plasmidfinder) { - call plasmidfinder_task.plasmidfinder { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename + if (genome_annotation == "prokka") { + call prokka_task.prokka { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } } - } - if (call_abricate) { - call abricate_task.abricate { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename, - database = abricate_db + if (genome_annotation == "bakta") { + call bakta_task.bakta { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } } - } - if (defined(qc_check_table)) { - call qc_check.qc_check_phb as qc_check_task { - input: - qc_check_table = qc_check_table, - expected_taxon = expected_taxon, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - num_reads_raw1 = read_QC_trim.fastq_scan_raw1, - num_reads_raw2 = read_QC_trim.fastq_scan_raw2, - num_reads_clean1 = read_QC_trim.fastq_scan_clean1, - num_reads_clean2 = read_QC_trim.fastq_scan_clean2, - r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, - r2_mean_q_raw = cg_pipeline_raw.r2_mean_q, - combined_mean_q_raw = cg_pipeline_raw.combined_mean_q, - r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, - r2_mean_readlength_raw = cg_pipeline_raw.r2_mean_readlength, - combined_mean_readlength_raw = cg_pipeline_raw.combined_mean_readlength, - r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, - r2_mean_q_clean = cg_pipeline_clean.r2_mean_q, - combined_mean_q_clean = cg_pipeline_clean.combined_mean_q, - r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, - r2_mean_readlength_clean = cg_pipeline_clean.r2_mean_readlength, - combined_mean_readlength_clean = cg_pipeline_clean.combined_mean_readlength, - est_coverage_raw = cg_pipeline_raw.est_coverage, - est_coverage_clean = cg_pipeline_clean.est_coverage, - midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, - midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - busco_results = busco.busco_results, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + if (call_plasmidfinder) { + call plasmidfinder_task.plasmidfinder { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } } - } - call merlin_magic_workflow.merlin_magic { - input: - merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), - assembly = shovill_pe.assembly_fasta, - samplename = samplename, - read1 = read_QC_trim.read1_clean, - read2 = read_QC_trim.read2_clean - } - if (defined(taxon_tables)) { - call terra_tools.export_taxon_tables { + if (call_abricate) { + call abricate_task.abricate { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename, + database = abricate_db + } + } + if (defined(qc_check_table)) { + call qc_check.qc_check_phb as qc_check_task { + input: + qc_check_table = qc_check_table, + expected_taxon = expected_taxon, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + num_reads_raw1 = read_QC_trim.fastq_scan_raw1, + num_reads_raw2 = read_QC_trim.fastq_scan_raw2, + num_reads_clean1 = read_QC_trim.fastq_scan_clean1, + num_reads_clean2 = read_QC_trim.fastq_scan_clean2, + r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, + r2_mean_q_raw = cg_pipeline_raw.r2_mean_q, + combined_mean_q_raw = cg_pipeline_raw.combined_mean_q, + r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, + r2_mean_readlength_raw = cg_pipeline_raw.r2_mean_readlength, + combined_mean_readlength_raw = cg_pipeline_raw.combined_mean_readlength, + r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, + r2_mean_q_clean = cg_pipeline_clean.r2_mean_q, + combined_mean_q_clean = cg_pipeline_clean.combined_mean_q, + r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, + r2_mean_readlength_clean = cg_pipeline_clean.r2_mean_readlength, + combined_mean_readlength_clean = cg_pipeline_clean.combined_mean_readlength, + est_coverage_raw = cg_pipeline_raw.est_coverage, + est_coverage_clean = cg_pipeline_clean.est_coverage, + midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, + midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + busco_results = busco.busco_results, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + } + } + call merlin_magic_workflow.merlin_magic { input: - terra_project = terra_project, - terra_workspace = terra_workspace, - sample_taxon = gambit.gambit_predicted_taxon, - taxon_tables = taxon_tables, + merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), + assembly = shovill_pe.assembly_fasta, samplename = samplename, - read1 = read1, - read2 = read2, - read1_clean = read_QC_trim.read1_clean, - read2_clean = read_QC_trim.read2_clean, - run_id = run_id, - collection_date = collection_date, - originating_lab = originating_lab, - city = city, - county = county, - zip = zip, - theiaprok_illumina_pe_version = version_capture.phb_version, - theiaprok_illumina_pe_analysis_date = version_capture.date, - seq_platform = seq_method, - num_reads_raw1 = read_QC_trim.fastq_scan_raw1, - num_reads_raw2 = read_QC_trim.fastq_scan_raw2, - num_reads_raw_pairs = read_QC_trim.fastq_scan_raw_pairs, - fastq_scan_version = read_QC_trim.fastq_scan_version, - num_reads_clean1 = read_QC_trim.fastq_scan_clean1, - num_reads_clean2 = read_QC_trim.fastq_scan_clean2, - num_reads_clean_pairs = read_QC_trim.fastq_scan_clean_pairs, - trimmomatic_version = read_QC_trim.trimmomatic_version, - fastp_version = read_QC_trim.fastp_version, - bbduk_docker = read_QC_trim.bbduk_docker, - r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, - r2_mean_q_raw = cg_pipeline_raw.r2_mean_q, - combined_mean_q_raw = cg_pipeline_raw.combined_mean_q, - r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, - r2_mean_readlength_raw = cg_pipeline_raw.r2_mean_readlength, - combined_mean_readlength_raw = cg_pipeline_raw.combined_mean_readlength, - r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, - r2_mean_q_clean = cg_pipeline_clean.r2_mean_q, - combined_mean_q_clean = cg_pipeline_clean.combined_mean_q, - r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, - r2_mean_readlength_clean = cg_pipeline_clean.r2_mean_readlength, - combined_mean_readlength_clean = cg_pipeline_clean.combined_mean_readlength, - assembly_fasta = shovill_pe.assembly_fasta, - contigs_gfa = shovill_pe.contigs_gfa, - shovill_pe_version = shovill_pe.shovill_version, - quast_report = quast.quast_report, - quast_version = quast.version, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - cg_pipeline_report_raw = cg_pipeline_raw.cg_pipeline_report, - cg_pipeline_docker = cg_pipeline_raw.cg_pipeline_docker, - est_coverage_raw = cg_pipeline_raw.est_coverage, - cg_pipeline_report_clean = cg_pipeline_clean.cg_pipeline_report, - est_coverage_clean = cg_pipeline_clean.est_coverage, - gambit_report = gambit.gambit_report_file, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, - gambit_closest_genomes = gambit.gambit_closest_genomes_file, - gambit_version = gambit.gambit_version, - gambit_db_version = gambit.gambit_db_version, - gambit_docker = gambit.gambit_docker, - busco_version = busco.busco_version, - busco_database = busco.busco_database, - busco_results = busco.busco_results, - busco_report = busco.busco_report, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, - ani_output_tsv = ani.ani_output_tsv, - ani_top_species_match = ani.ani_top_species_match, - ani_mummer_version = ani.ani_mummer_version, - ani_docker = ani.ani_docker, - kmerfinder_docker = kmerfinder.kmerfinder_docker, - kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, - kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, - kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, - kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, - kmerfinder_database = kmerfinder.kmerfinder_database, - amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, - amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, - amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, - amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, - amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, - amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, - amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, - amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, - amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, - amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, - amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, - amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, - resfinder_pheno_table = resfinder_task.resfinder_pheno_table, - resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, - resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, - resfinder_results = resfinder_task.resfinder_results_tab, - resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, - resfinder_pointfinder_results = resfinder_task.pointfinder_results, - resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, - resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, - resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, - resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, - resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, - resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, - resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, - resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, - resfinder_db_version = resfinder_task.resfinder_db_version, - resfinder_docker = resfinder_task.resfinder_docker, - ts_mlst_results = ts_mlst.ts_mlst_results, - ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, - ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, - ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, - ts_mlst_version = ts_mlst.ts_mlst_version, - ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, - ts_mlst_docker = ts_mlst.ts_mlst_docker, - serotypefinder_report = merlin_magic.serotypefinder_report, - serotypefinder_docker = merlin_magic.serotypefinder_docker, - serotypefinder_serotype = merlin_magic.serotypefinder_serotype, - ectyper_results = merlin_magic.ectyper_results, - ectyper_version = merlin_magic.ectyper_version, - ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, - shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, - shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, - shigatyper_notes = merlin_magic.shigatyper_notes, - shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, - shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, - shigatyper_version = merlin_magic.shigatyper_version, - shigatyper_docker = merlin_magic.shigatyper_docker, - shigeifinder_report = merlin_magic.shigeifinder_report, - shigeifinder_docker = merlin_magic.shigeifinder_docker, - shigeifinder_version = merlin_magic.shigeifinder_version, - shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, - shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, - shigeifinder_cluster = merlin_magic.shigeifinder_cluster, - shigeifinder_serotype = merlin_magic.shigeifinder_serotype, - shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, - shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, - shigeifinder_notes = merlin_magic.shigeifinder_notes, - shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, - shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, - shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, - shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, - shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, - shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, - shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, - shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, - shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, - shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, - virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, - virulencefinder_docker = merlin_magic.virulencefinder_docker, - virulencefinder_hits = merlin_magic.virulencefinder_hits, - sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, - sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, - sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, - sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, - sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, - sonneityping_species = merlin_magic.sonneityping_species, - sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, - sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, - sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, - lissero_results = merlin_magic.lissero_results, - lissero_version = merlin_magic.lissero_version, - lissero_serotype = merlin_magic.lissero_serotype, - sistr_results = merlin_magic.sistr_results, - sistr_allele_json = merlin_magic.sistr_allele_json, - sistr_allele_fasta = merlin_magic.sistr_allele_fasta, - sistr_cgmlst = merlin_magic.sistr_cgmlst, - sistr_version = merlin_magic.sistr_version, - sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, - seqsero2_report = merlin_magic.seqsero2_report, - seqsero2_version = merlin_magic.seqsero2_version, - seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, - seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, - seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, - genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, - genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, - genotyphi_version = merlin_magic.genotyphi_version, - genotyphi_species = merlin_magic.genotyphi_species, - genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, - genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, - genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, - kleborate_output_file = merlin_magic.kleborate_output_file, - kleborate_version = merlin_magic.kleborate_version, - kleborate_docker = merlin_magic.kleborate_docker, - kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, - kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, - kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, - kleborate_klocus = merlin_magic.kleborate_klocus, - kleborate_ktype = merlin_magic.kleborate_ktype, - kleborate_olocus = merlin_magic.kleborate_olocus, - kleborate_otype = merlin_magic.kleborate_otype, - kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, - kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, - kleborate_virulence_score = merlin_magic.kleborate_virulence_score, - kleborate_resistance_score = merlin_magic.kleborate_resistance_score, - ngmaster_tsv = merlin_magic.ngmaster_tsv, - ngmaster_version = merlin_magic.ngmaster_version, - ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, - ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, - ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, - ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, - ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, - ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, - ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, - ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, - ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, - ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, - ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, - meningotype_tsv = merlin_magic.meningotype_tsv, - meningotype_version = merlin_magic.meningotype_version, - meningotype_serogroup = merlin_magic.meningotype_serogroup, - meningotype_PorA = merlin_magic.meningotype_PorA, - meningotype_FetA = merlin_magic.meningotype_FetA, - meningotype_PorB = merlin_magic.meningotype_PorB, - meningotype_fHbp = merlin_magic.meningotype_fHbp, - meningotype_NHBA = merlin_magic.meningotype_NHBA, - meningotype_NadA = merlin_magic.meningotype_NadA, - meningotype_BAST = merlin_magic.meningotype_BAST, - kaptive_output_file_k = merlin_magic.kaptive_output_file_k, - kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, - kaptive_version = merlin_magic.kaptive_version, - kaptive_k_locus = merlin_magic.kaptive_k_match, - kaptive_k_type = merlin_magic.kaptive_k_type, - kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, - kaptive_oc_locus = merlin_magic.kaptive_oc_match, - kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, - abricate_results_tsv = abricate.abricate_results, - abricate_genes = abricate.abricate_genes, - abricate_database = abricate.abricate_database, - abricate_version = abricate.abricate_version, - abricate_docker = abricate.abricate_docker, - abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, - abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, - abricate_abaum_database = merlin_magic.abricate_abaum_database, - abricate_abaum_version = merlin_magic.abricate_abaum_version, - abricate_abaum_docker = merlin_magic.abricate_abaum_docker, - tbprofiler_output_file = merlin_magic.tbprofiler_output_file, - tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, - tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, - tbprofiler_version = merlin_magic.tbprofiler_version, - tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, - tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, - tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, - tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, - legsta_results = merlin_magic.legsta_results, - legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, - legsta_version = merlin_magic.legsta_version, - prokka_gff = prokka.prokka_gff, - prokka_gbk = prokka.prokka_gbk, - prokka_sqn = prokka.prokka_sqn, - bakta_gbff = bakta.bakta_gbff, - bakta_gff3 = bakta.bakta_gff3, - bakta_tsv = bakta.bakta_tsv, - bakta_summary = bakta.bakta_txt, - bakta_version = bakta.bakta_version, - plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, - plasmidfinder_results = plasmidfinder.plasmidfinder_results, - plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, - plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, - plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, - pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, - pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, - pbptyper_version = merlin_magic.pbptyper_version, - pbptyper_docker = merlin_magic.pbptyper_docker, - poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, - poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, - poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, - poppunk_version = merlin_magic.poppunk_version, - poppunk_docker = merlin_magic.poppunk_docker, - spatyper_tsv = merlin_magic.spatyper_tsv, - spatyper_docker = merlin_magic.spatyper_docker, - spatyper_repeats = merlin_magic.spatyper_repeats, - spatyper_type = merlin_magic.spatyper_type, - spatyper_version = merlin_magic.spatyper_version, - staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, - staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, - staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, - staphopiasccmec_version = merlin_magic.staphopiasccmec_version, - staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, - agrvate_summary = merlin_magic.agrvate_summary, - agrvate_results = merlin_magic.agrvate_results, - agrvate_agr_group = merlin_magic.agrvate_agr_group, - agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, - agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, - agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, - agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, - agrvate_version = merlin_magic.agrvate_version, - agrvate_docker = merlin_magic.agrvate_docker, - seroba_version = merlin_magic.seroba_version, - seroba_docker = merlin_magic.seroba_docker, - seroba_serotype = merlin_magic.seroba_serotype, - seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype, - seroba_ariba_identity = merlin_magic.seroba_ariba_identity, - seroba_details = merlin_magic.seroba_details, - emmtyper_emm_type = merlin_magic.emmtyper_emm_type, - emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, - emmtyper_version = merlin_magic.emmtyper_version, - emmtyper_docker = merlin_magic.emmtyper_docker, - emmtypingtool_emm_type = merlin_magic.emmtypingtool_emm_type, - emmtypingtool_results_xml = merlin_magic.emmtypingtool_results_xml, - emmtypingtool_version = merlin_magic.emmtypingtool_version, - emmtypingtool_docker = merlin_magic.emmtypingtool_docker, - hicap_serotype = merlin_magic.hicap_serotype, - hicap_genes = merlin_magic.hicap_genes, - hicap_results_tsv = merlin_magic.hicap_results_tsv, - hicap_version = merlin_magic.hicap_version, - hicap_docker = merlin_magic.hicap_docker, - midas_docker = read_QC_trim.midas_docker, - midas_report = read_QC_trim.midas_report, - midas_primary_genus = read_QC_trim.midas_primary_genus, - midas_secondary_genus = read_QC_trim.midas_secondary_genus, - midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, - midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, - kraken2_version = read_QC_trim.kraken_version, - kraken2_report = read_QC_trim.kraken_report, - pasty_serogroup = merlin_magic.pasty_serogroup, - pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, - pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, - pasty_summary_tsv = merlin_magic.pasty_summary_tsv, - pasty_blast_hits = merlin_magic.pasty_blast_hits, - pasty_all_serogroups = merlin_magic.pasty_all_serogroups, - pasty_version = merlin_magic.pasty_version, - pasty_docker = merlin_magic.pasty_docker, - pasty_comment = merlin_magic.pasty_comment, - qc_check = qc_check_task.qc_check, - qc_standard = qc_check_task.qc_standard, - srst2_vibrio_detailed_tsv = merlin_magic.srst2_vibrio_detailed_tsv, - srst2_vibrio_docker = merlin_magic.srst2_vibrio_docker, - srst2_vibrio_database = merlin_magic.srst2_vibrio_database, - srst2_vibrio_version = merlin_magic.srst2_vibrio_version, - srst2_vibrio_ctxA = merlin_magic.srst2_vibrio_ctxA, - srst2_vibrio_ompW = merlin_magic.srst2_vibrio_ompW, - srst2_vibrio_toxR = merlin_magic.srst2_vibrio_toxR, - srst2_vibrio_serogroup = merlin_magic.srst2_vibrio_serogroup, - srst2_vibrio_biotype = merlin_magic.srst2_vibrio_biotype, - abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, - abricate_vibrio_database = merlin_magic.abricate_vibrio_database, - abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, - abricate_vibrio_version = merlin_magic.abricate_vibrio_version, - abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, - abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, - abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, - abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, - abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + read1 = read_QC_trim.read1_clean, + read2 = read_QC_trim.read2_clean + } + if (defined(taxon_tables)) { + call terra_tools.export_taxon_tables { + input: + terra_project = terra_project, + terra_workspace = terra_workspace, + sample_taxon = gambit.gambit_predicted_taxon, + taxon_tables = taxon_tables, + samplename = samplename, + read1 = read1, + read2 = read2, + read1_clean = read_QC_trim.read1_clean, + read2_clean = read_QC_trim.read2_clean, + run_id = run_id, + collection_date = collection_date, + originating_lab = originating_lab, + city = city, + county = county, + zip = zip, + theiaprok_illumina_pe_version = version_capture.phb_version, + theiaprok_illumina_pe_analysis_date = version_capture.date, + seq_platform = seq_method, + num_reads_raw1 = read_QC_trim.fastq_scan_raw1, + num_reads_raw2 = read_QC_trim.fastq_scan_raw2, + num_reads_raw_pairs = read_QC_trim.fastq_scan_raw_pairs, + fastq_scan_version = read_QC_trim.fastq_scan_version, + num_reads_clean1 = read_QC_trim.fastq_scan_clean1, + num_reads_clean2 = read_QC_trim.fastq_scan_clean2, + num_reads_clean_pairs = read_QC_trim.fastq_scan_clean_pairs, + trimmomatic_version = read_QC_trim.trimmomatic_version, + fastp_version = read_QC_trim.fastp_version, + bbduk_docker = read_QC_trim.bbduk_docker, + r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, + r2_mean_q_raw = cg_pipeline_raw.r2_mean_q, + combined_mean_q_raw = cg_pipeline_raw.combined_mean_q, + r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, + r2_mean_readlength_raw = cg_pipeline_raw.r2_mean_readlength, + combined_mean_readlength_raw = cg_pipeline_raw.combined_mean_readlength, + r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, + r2_mean_q_clean = cg_pipeline_clean.r2_mean_q, + combined_mean_q_clean = cg_pipeline_clean.combined_mean_q, + r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, + r2_mean_readlength_clean = cg_pipeline_clean.r2_mean_readlength, + combined_mean_readlength_clean = cg_pipeline_clean.combined_mean_readlength, + assembly_fasta = shovill_pe.assembly_fasta, + contigs_gfa = shovill_pe.contigs_gfa, + shovill_pe_version = shovill_pe.shovill_version, + quast_report = quast.quast_report, + quast_version = quast.version, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + cg_pipeline_report_raw = cg_pipeline_raw.cg_pipeline_report, + cg_pipeline_docker = cg_pipeline_raw.cg_pipeline_docker, + est_coverage_raw = cg_pipeline_raw.est_coverage, + cg_pipeline_report_clean = cg_pipeline_clean.cg_pipeline_report, + est_coverage_clean = cg_pipeline_clean.est_coverage, + gambit_report = gambit.gambit_report_file, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, + gambit_closest_genomes = gambit.gambit_closest_genomes_file, + gambit_version = gambit.gambit_version, + gambit_db_version = gambit.gambit_db_version, + gambit_docker = gambit.gambit_docker, + busco_version = busco.busco_version, + busco_database = busco.busco_database, + busco_results = busco.busco_results, + busco_report = busco.busco_report, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, + ani_output_tsv = ani.ani_output_tsv, + ani_top_species_match = ani.ani_top_species_match, + ani_mummer_version = ani.ani_mummer_version, + ani_docker = ani.ani_docker, + kmerfinder_docker = kmerfinder.kmerfinder_docker, + kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, + kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, + kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, + kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, + kmerfinder_database = kmerfinder.kmerfinder_database, + amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, + amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, + amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, + amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, + amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, + amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, + amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, + amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, + amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, + amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, + amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, + amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, + resfinder_pheno_table = resfinder_task.resfinder_pheno_table, + resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, + resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, + resfinder_results = resfinder_task.resfinder_results_tab, + resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, + resfinder_pointfinder_results = resfinder_task.pointfinder_results, + resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, + resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, + resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, + resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, + resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, + resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, + resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, + resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, + resfinder_db_version = resfinder_task.resfinder_db_version, + resfinder_docker = resfinder_task.resfinder_docker, + ts_mlst_results = ts_mlst.ts_mlst_results, + ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, + ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, + ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, + ts_mlst_version = ts_mlst.ts_mlst_version, + ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, + ts_mlst_docker = ts_mlst.ts_mlst_docker, + serotypefinder_report = merlin_magic.serotypefinder_report, + serotypefinder_docker = merlin_magic.serotypefinder_docker, + serotypefinder_serotype = merlin_magic.serotypefinder_serotype, + ectyper_results = merlin_magic.ectyper_results, + ectyper_version = merlin_magic.ectyper_version, + ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, + shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, + shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, + shigatyper_notes = merlin_magic.shigatyper_notes, + shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, + shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, + shigatyper_version = merlin_magic.shigatyper_version, + shigatyper_docker = merlin_magic.shigatyper_docker, + shigeifinder_report = merlin_magic.shigeifinder_report, + shigeifinder_docker = merlin_magic.shigeifinder_docker, + shigeifinder_version = merlin_magic.shigeifinder_version, + shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, + shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, + shigeifinder_cluster = merlin_magic.shigeifinder_cluster, + shigeifinder_serotype = merlin_magic.shigeifinder_serotype, + shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, + shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, + shigeifinder_notes = merlin_magic.shigeifinder_notes, + shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, + shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, + shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, + shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, + shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, + shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, + shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, + shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, + shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, + shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, + virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, + virulencefinder_docker = merlin_magic.virulencefinder_docker, + virulencefinder_hits = merlin_magic.virulencefinder_hits, + sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, + sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, + sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, + sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, + sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, + sonneityping_species = merlin_magic.sonneityping_species, + sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, + sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, + sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, + lissero_results = merlin_magic.lissero_results, + lissero_version = merlin_magic.lissero_version, + lissero_serotype = merlin_magic.lissero_serotype, + sistr_results = merlin_magic.sistr_results, + sistr_allele_json = merlin_magic.sistr_allele_json, + sistr_allele_fasta = merlin_magic.sistr_allele_fasta, + sistr_cgmlst = merlin_magic.sistr_cgmlst, + sistr_version = merlin_magic.sistr_version, + sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, + seqsero2_report = merlin_magic.seqsero2_report, + seqsero2_version = merlin_magic.seqsero2_version, + seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, + seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, + seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, + genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, + genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, + genotyphi_version = merlin_magic.genotyphi_version, + genotyphi_species = merlin_magic.genotyphi_species, + genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, + genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, + genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, + kleborate_output_file = merlin_magic.kleborate_output_file, + kleborate_version = merlin_magic.kleborate_version, + kleborate_docker = merlin_magic.kleborate_docker, + kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, + kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, + kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, + kleborate_klocus = merlin_magic.kleborate_klocus, + kleborate_ktype = merlin_magic.kleborate_ktype, + kleborate_olocus = merlin_magic.kleborate_olocus, + kleborate_otype = merlin_magic.kleborate_otype, + kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, + kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, + ngmaster_tsv = merlin_magic.ngmaster_tsv, + ngmaster_version = merlin_magic.ngmaster_version, + ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, + ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, + ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, + ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, + ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, + ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, + ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, + ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, + ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, + ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, + ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, + meningotype_tsv = merlin_magic.meningotype_tsv, + meningotype_version = merlin_magic.meningotype_version, + meningotype_serogroup = merlin_magic.meningotype_serogroup, + meningotype_PorA = merlin_magic.meningotype_PorA, + meningotype_FetA = merlin_magic.meningotype_FetA, + meningotype_PorB = merlin_magic.meningotype_PorB, + meningotype_fHbp = merlin_magic.meningotype_fHbp, + meningotype_NHBA = merlin_magic.meningotype_NHBA, + meningotype_NadA = merlin_magic.meningotype_NadA, + meningotype_BAST = merlin_magic.meningotype_BAST, + kaptive_output_file_k = merlin_magic.kaptive_output_file_k, + kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, + kaptive_version = merlin_magic.kaptive_version, + kaptive_k_locus = merlin_magic.kaptive_k_match, + kaptive_k_type = merlin_magic.kaptive_k_type, + kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, + kaptive_oc_locus = merlin_magic.kaptive_oc_match, + kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, + abricate_results_tsv = abricate.abricate_results, + abricate_genes = abricate.abricate_genes, + abricate_database = abricate.abricate_database, + abricate_version = abricate.abricate_version, + abricate_docker = abricate.abricate_docker, + abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, + abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, + abricate_abaum_database = merlin_magic.abricate_abaum_database, + abricate_abaum_version = merlin_magic.abricate_abaum_version, + abricate_abaum_docker = merlin_magic.abricate_abaum_docker, + tbprofiler_output_file = merlin_magic.tbprofiler_output_file, + tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, + tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, + tbprofiler_version = merlin_magic.tbprofiler_version, + tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, + tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, + tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, + tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, + legsta_results = merlin_magic.legsta_results, + legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, + legsta_version = merlin_magic.legsta_version, + prokka_gff = prokka.prokka_gff, + prokka_gbk = prokka.prokka_gbk, + prokka_sqn = prokka.prokka_sqn, + bakta_gbff = bakta.bakta_gbff, + bakta_gff3 = bakta.bakta_gff3, + bakta_tsv = bakta.bakta_tsv, + bakta_summary = bakta.bakta_txt, + bakta_version = bakta.bakta_version, + plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, + plasmidfinder_results = plasmidfinder.plasmidfinder_results, + plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, + plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, + plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, + pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, + pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, + pbptyper_version = merlin_magic.pbptyper_version, + pbptyper_docker = merlin_magic.pbptyper_docker, + poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, + poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, + poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, + poppunk_version = merlin_magic.poppunk_version, + poppunk_docker = merlin_magic.poppunk_docker, + spatyper_tsv = merlin_magic.spatyper_tsv, + spatyper_docker = merlin_magic.spatyper_docker, + spatyper_repeats = merlin_magic.spatyper_repeats, + spatyper_type = merlin_magic.spatyper_type, + spatyper_version = merlin_magic.spatyper_version, + staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, + staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, + staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, + staphopiasccmec_version = merlin_magic.staphopiasccmec_version, + staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, + agrvate_summary = merlin_magic.agrvate_summary, + agrvate_results = merlin_magic.agrvate_results, + agrvate_agr_group = merlin_magic.agrvate_agr_group, + agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, + agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, + agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, + agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, + agrvate_version = merlin_magic.agrvate_version, + agrvate_docker = merlin_magic.agrvate_docker, + seroba_version = merlin_magic.seroba_version, + seroba_docker = merlin_magic.seroba_docker, + seroba_serotype = merlin_magic.seroba_serotype, + seroba_ariba_serotype = merlin_magic.seroba_ariba_serotype, + seroba_ariba_identity = merlin_magic.seroba_ariba_identity, + seroba_details = merlin_magic.seroba_details, + emmtyper_emm_type = merlin_magic.emmtyper_emm_type, + emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, + emmtyper_version = merlin_magic.emmtyper_version, + emmtyper_docker = merlin_magic.emmtyper_docker, + emmtypingtool_emm_type = merlin_magic.emmtypingtool_emm_type, + emmtypingtool_results_xml = merlin_magic.emmtypingtool_results_xml, + emmtypingtool_version = merlin_magic.emmtypingtool_version, + emmtypingtool_docker = merlin_magic.emmtypingtool_docker, + hicap_serotype = merlin_magic.hicap_serotype, + hicap_genes = merlin_magic.hicap_genes, + hicap_results_tsv = merlin_magic.hicap_results_tsv, + hicap_version = merlin_magic.hicap_version, + hicap_docker = merlin_magic.hicap_docker, + midas_docker = read_QC_trim.midas_docker, + midas_report = read_QC_trim.midas_report, + midas_primary_genus = read_QC_trim.midas_primary_genus, + midas_secondary_genus = read_QC_trim.midas_secondary_genus, + midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, + midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, + kraken2_version = read_QC_trim.kraken_version, + kraken2_report = read_QC_trim.kraken_report, + pasty_serogroup = merlin_magic.pasty_serogroup, + pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, + pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, + pasty_summary_tsv = merlin_magic.pasty_summary_tsv, + pasty_blast_hits = merlin_magic.pasty_blast_hits, + pasty_all_serogroups = merlin_magic.pasty_all_serogroups, + pasty_version = merlin_magic.pasty_version, + pasty_docker = merlin_magic.pasty_docker, + pasty_comment = merlin_magic.pasty_comment, + qc_check = qc_check_task.qc_check, + qc_standard = qc_check_task.qc_standard, + srst2_vibrio_detailed_tsv = merlin_magic.srst2_vibrio_detailed_tsv, + srst2_vibrio_docker = merlin_magic.srst2_vibrio_docker, + srst2_vibrio_database = merlin_magic.srst2_vibrio_database, + srst2_vibrio_version = merlin_magic.srst2_vibrio_version, + srst2_vibrio_ctxA = merlin_magic.srst2_vibrio_ctxA, + srst2_vibrio_ompW = merlin_magic.srst2_vibrio_ompW, + srst2_vibrio_toxR = merlin_magic.srst2_vibrio_toxR, + srst2_vibrio_serogroup = merlin_magic.srst2_vibrio_serogroup, + srst2_vibrio_biotype = merlin_magic.srst2_vibrio_biotype, + abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, + abricate_vibrio_database = merlin_magic.abricate_vibrio_database, + abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, + abricate_vibrio_version = merlin_magic.abricate_vibrio_version, + abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, + abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, + abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, + abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, + abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + } } } } diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index a5305463c..1b6aa9f91 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -53,6 +53,7 @@ workflow theiaprok_illumina_se { Int trim_quality_min_score = 30 Int trim_window_size = 4 # module options + Boolean perform_characterization = true # by default run all characterization steps Boolean call_ani = false # by default do not call ANI task, but user has ability to enable this task if working with enteric pathogens or supply their own high-quality reference genome Boolean call_kmerfinder = false Boolean call_resfinder = false @@ -135,422 +136,424 @@ workflow theiaprok_illumina_se { assembly = shovill_se.assembly_fasta, samplename = samplename } - if (call_ani) { - call ani_task.animummer as ani { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename + if (perform_characterization) { + if (call_ani) { + call ani_task.animummer as ani { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + } } - } - if (call_kmerfinder) { - call kmerfinder_task.kmerfinder_bacteria as kmerfinder { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename + if (call_kmerfinder) { + call kmerfinder_task.kmerfinder_bacteria as kmerfinder { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + } } - } - call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename, - organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) - } - if (call_resfinder) { - call resfinder.resfinder as resfinder_task { + call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { input: assembly = shovill_se.assembly_fasta, samplename = samplename, organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) } - } - call ts_mlst_task.ts_mlst { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename - } - if (genome_annotation == "prokka") { - call prokka_task.prokka { - input: + if (call_resfinder) { + call resfinder.resfinder as resfinder_task { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename, + organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) + } + } + call ts_mlst_task.ts_mlst { + input: assembly = shovill_se.assembly_fasta, samplename = samplename } - } - if (genome_annotation == "bakta") { - call bakta_task.bakta { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename + if (genome_annotation == "prokka") { + call prokka_task.prokka { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + } } - } - if (call_plasmidfinder) { - call plasmidfinder_task.plasmidfinder { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename + if (genome_annotation == "bakta") { + call bakta_task.bakta { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + } } - } - if (call_abricate) { - call abricate_task.abricate { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename, - database = abricate_db + if (call_plasmidfinder) { + call plasmidfinder_task.plasmidfinder { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + } } - } - if (defined(qc_check_table)) { - call qc_check.qc_check_phb as qc_check_task { - input: - qc_check_table = qc_check_table, - expected_taxon = expected_taxon, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - num_reads_raw1 = read_QC_trim.fastq_scan_raw1, - num_reads_clean1 = read_QC_trim.fastq_scan_clean1, - r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, - r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, - r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, - r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, - est_coverage_raw = cg_pipeline_raw.est_coverage, - est_coverage_clean = cg_pipeline_clean.est_coverage, - midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, - midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - busco_results = busco.busco_results, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + if (call_abricate) { + call abricate_task.abricate { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename, + database = abricate_db + } } - } - call merlin_magic_workflow.merlin_magic { - input: - merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), - assembly = shovill_se.assembly_fasta, - samplename = samplename, - read1 = read_QC_trim.read1_clean, - paired_end = false - } - if (defined(taxon_tables)) { - call terra_tools.export_taxon_tables { + if (defined(qc_check_table)) { + call qc_check.qc_check_phb as qc_check_task { + input: + qc_check_table = qc_check_table, + expected_taxon = expected_taxon, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + num_reads_raw1 = read_QC_trim.fastq_scan_raw1, + num_reads_clean1 = read_QC_trim.fastq_scan_clean1, + r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, + r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, + r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, + r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, + est_coverage_raw = cg_pipeline_raw.est_coverage, + est_coverage_clean = cg_pipeline_clean.est_coverage, + midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, + midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + busco_results = busco.busco_results, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + } + } + call merlin_magic_workflow.merlin_magic { input: - terra_project = terra_project, - terra_workspace = terra_workspace, - sample_taxon = gambit.gambit_predicted_taxon, - taxon_tables = taxon_tables, + merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), + assembly = shovill_se.assembly_fasta, samplename = samplename, - read1 = read1, - read1_clean = read_QC_trim.read1_clean, - run_id = run_id, - collection_date = collection_date, - originating_lab = originating_lab, - city = city, - county = county, - zip = zip, - theiaprok_illumina_se_version = version_capture.phb_version, - theiaprok_illumina_se_analysis_date = version_capture.date, - seq_platform = seq_method, - num_reads_raw1 = read_QC_trim.fastq_scan_raw1, - fastq_scan_version = read_QC_trim.fastq_scan_version, - num_reads_clean1 = read_QC_trim.fastq_scan_clean1, - trimmomatic_version = read_QC_trim.trimmomatic_version, - fastp_version = read_QC_trim.fastp_version, - bbduk_docker = read_QC_trim.bbduk_docker, - r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, - r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, - r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, - r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, - assembly_fasta = shovill_se.assembly_fasta, - contigs_gfa = shovill_se.contigs_gfa, - shovill_se_version = shovill_se.shovill_version, - quast_report = quast.quast_report, - quast_version = quast.version, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - cg_pipeline_report_raw = cg_pipeline_raw.cg_pipeline_report, - cg_pipeline_docker = cg_pipeline_raw.cg_pipeline_docker, - est_coverage_raw = cg_pipeline_raw.est_coverage, - cg_pipeline_report_clean = cg_pipeline_clean.cg_pipeline_report, - est_coverage_clean = cg_pipeline_clean.est_coverage, - gambit_report = gambit.gambit_report_file, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, - gambit_closest_genomes = gambit.gambit_closest_genomes_file, - gambit_version = gambit.gambit_version, - gambit_db_version = gambit.gambit_db_version, - gambit_docker = gambit.gambit_docker, - busco_version = busco.busco_version, - busco_database = busco.busco_database, - busco_results = busco.busco_results, - busco_report = busco.busco_report, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, - ani_output_tsv = ani.ani_output_tsv, - ani_top_species_match = ani.ani_top_species_match, - ani_mummer_version = ani.ani_mummer_version, - ani_docker = ani.ani_docker, - kmerfinder_docker = kmerfinder.kmerfinder_docker, - kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, - kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, - kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, - kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, - kmerfinder_database = kmerfinder.kmerfinder_database, - amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, - amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, - amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, - amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, - amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, - amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, - amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, - amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, - amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, - amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, - amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, - amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, - resfinder_pheno_table = resfinder_task.resfinder_pheno_table, - resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, - resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, - resfinder_results = resfinder_task.resfinder_results_tab, - resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, - resfinder_pointfinder_results = resfinder_task.pointfinder_results, - resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, - resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, - resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, - resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, - resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, - resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, - resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, - resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, - resfinder_db_version = resfinder_task.resfinder_db_version, - resfinder_docker = resfinder_task.resfinder_docker, - ts_mlst_results = ts_mlst.ts_mlst_results, - ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, - ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, - ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, - ts_mlst_version = ts_mlst.ts_mlst_version, - ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, - ts_mlst_docker = ts_mlst.ts_mlst_docker, - serotypefinder_report = merlin_magic.serotypefinder_report, - serotypefinder_docker = merlin_magic.serotypefinder_docker, - serotypefinder_serotype = merlin_magic.serotypefinder_serotype, - ectyper_results = merlin_magic.ectyper_results, - ectyper_version = merlin_magic.ectyper_version, - ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, - shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, - shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, - shigatyper_notes = merlin_magic.shigatyper_notes, - shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, - shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, - shigatyper_version = merlin_magic.shigatyper_version, - shigatyper_docker = merlin_magic.shigatyper_docker, - shigeifinder_report = merlin_magic.shigeifinder_report, - shigeifinder_docker = merlin_magic.shigeifinder_docker, - shigeifinder_version = merlin_magic.shigeifinder_version, - shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, - shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, - shigeifinder_cluster = merlin_magic.shigeifinder_cluster, - shigeifinder_serotype = merlin_magic.shigeifinder_serotype, - shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, - shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, - shigeifinder_notes = merlin_magic.shigeifinder_notes, - shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, - shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, - shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, - shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, - shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, - shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, - shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, - shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, - shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, - shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, - virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, - virulencefinder_docker = merlin_magic.virulencefinder_docker, - virulencefinder_hits = merlin_magic.virulencefinder_hits, - sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, - sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, - sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, - sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, - sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, - sonneityping_species = merlin_magic.sonneityping_species, - sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, - sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, - sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, - lissero_results = merlin_magic.lissero_results, - lissero_version = merlin_magic.lissero_version, - lissero_serotype = merlin_magic.lissero_serotype, - sistr_results = merlin_magic.sistr_results, - sistr_allele_json = merlin_magic.sistr_allele_json, - sistr_allele_fasta = merlin_magic.sistr_allele_fasta, - sistr_cgmlst = merlin_magic.sistr_cgmlst, - sistr_version = merlin_magic.sistr_version, - sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, - seqsero2_report = merlin_magic.seqsero2_report, - seqsero2_version = merlin_magic.seqsero2_version, - seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, - seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, - seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, - genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, - genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, - genotyphi_version = merlin_magic.genotyphi_version, - genotyphi_species = merlin_magic.genotyphi_species, - genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, - genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, - genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, - kleborate_output_file = merlin_magic.kleborate_output_file, - kleborate_version = merlin_magic.kleborate_version, - kleborate_docker = merlin_magic.kleborate_docker, - kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, - kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, - kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, - kleborate_klocus = merlin_magic.kleborate_klocus, - kleborate_ktype = merlin_magic.kleborate_ktype, - kleborate_olocus = merlin_magic.kleborate_olocus, - kleborate_otype = merlin_magic.kleborate_otype, - kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, - kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, - kleborate_virulence_score = merlin_magic.kleborate_virulence_score, - kleborate_resistance_score = merlin_magic.kleborate_resistance_score, - ngmaster_tsv = merlin_magic.ngmaster_tsv, - ngmaster_version = merlin_magic.ngmaster_version, - ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, - ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, - ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, - ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, - ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, - ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, - ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, - ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, - ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, - ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, - ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, - meningotype_tsv = merlin_magic.meningotype_tsv, - meningotype_version = merlin_magic.meningotype_version, - meningotype_serogroup = merlin_magic.meningotype_serogroup, - meningotype_PorA = merlin_magic.meningotype_PorA, - meningotype_FetA = merlin_magic.meningotype_FetA, - meningotype_PorB = merlin_magic.meningotype_PorB, - meningotype_fHbp = merlin_magic.meningotype_fHbp, - meningotype_NHBA = merlin_magic.meningotype_NHBA, - meningotype_NadA = merlin_magic.meningotype_NadA, - meningotype_BAST = merlin_magic.meningotype_BAST, - kaptive_output_file_k = merlin_magic.kaptive_output_file_k, - kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, - kaptive_version = merlin_magic.kaptive_version, - kaptive_k_locus = merlin_magic.kaptive_k_match, - kaptive_k_type = merlin_magic.kaptive_k_type, - kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, - kaptive_oc_locus = merlin_magic.kaptive_oc_match, - kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, - abricate_results_tsv = abricate.abricate_results, - abricate_genes = abricate.abricate_genes, - abricate_database = abricate.abricate_database, - abricate_version = abricate.abricate_version, - abricate_docker = abricate.abricate_docker, - abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, - abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, - abricate_abaum_database = merlin_magic.abricate_abaum_database, - abricate_abaum_version = merlin_magic.abricate_abaum_version, - abricate_abaum_docker = merlin_magic.abricate_abaum_docker, - tbprofiler_output_file = merlin_magic.tbprofiler_output_file, - tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, - tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, - tbprofiler_version = merlin_magic.tbprofiler_version, - tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, - tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, - tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, - tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, - legsta_results = merlin_magic.legsta_results, - legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, - legsta_version = merlin_magic.legsta_version, - prokka_gff = prokka.prokka_gff, - prokka_gbk = prokka.prokka_gbk, - prokka_sqn = prokka.prokka_sqn, - bakta_gbff = bakta.bakta_gbff, - bakta_gff3 = bakta.bakta_gff3, - bakta_tsv = bakta.bakta_tsv, - bakta_summary = bakta.bakta_txt, - bakta_version = bakta.bakta_version, - plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, - plasmidfinder_results = plasmidfinder.plasmidfinder_results, - plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, - plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, - plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, - pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, - pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, - pbptyper_version = merlin_magic.pbptyper_version, - pbptyper_docker = merlin_magic.pbptyper_docker, - poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, - poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, - poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, - poppunk_version = merlin_magic.poppunk_version, - poppunk_docker = merlin_magic.poppunk_docker, - spatyper_tsv = merlin_magic.spatyper_tsv, - spatyper_docker = merlin_magic.spatyper_docker, - spatyper_repeats = merlin_magic.spatyper_repeats, - spatyper_type = merlin_magic.spatyper_type, - spatyper_version = merlin_magic.spatyper_version, - staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, - staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, - staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, - staphopiasccmec_version = merlin_magic.staphopiasccmec_version, - staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, - agrvate_summary = merlin_magic.agrvate_summary, - agrvate_results = merlin_magic.agrvate_results, - agrvate_agr_group = merlin_magic.agrvate_agr_group, - agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, - agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, - agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, - agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, - agrvate_version = merlin_magic.agrvate_version, - agrvate_docker = merlin_magic.agrvate_docker, - emmtyper_emm_type = merlin_magic.emmtyper_emm_type, - emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, - emmtyper_version = merlin_magic.emmtyper_version, - emmtyper_docker = merlin_magic.emmtyper_docker, - midas_docker = read_QC_trim.midas_docker, - midas_report = read_QC_trim.midas_report, - midas_primary_genus = read_QC_trim.midas_primary_genus, - midas_secondary_genus = read_QC_trim.midas_secondary_genus, - midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, - midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, - kraken2_version = read_QC_trim.kraken_version, - kraken2_docker = read_QC_trim.kraken_docker, - kraken2_report = read_QC_trim.kraken_report, - pasty_serogroup = merlin_magic.pasty_serogroup, - pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, - pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, - pasty_summary_tsv = merlin_magic.pasty_summary_tsv, - pasty_blast_hits = merlin_magic.pasty_blast_hits, - pasty_all_serogroups = merlin_magic.pasty_all_serogroups, - pasty_version = merlin_magic.pasty_version, - pasty_docker = merlin_magic.pasty_docker, - pasty_comment = merlin_magic.pasty_comment, - hicap_serotype = merlin_magic.hicap_serotype, - hicap_genes = merlin_magic.hicap_genes, - hicap_results_tsv = merlin_magic.hicap_results_tsv, - hicap_version = merlin_magic.hicap_version, - hicap_docker = merlin_magic.hicap_docker, - srst2_vibrio_detailed_tsv = merlin_magic.srst2_vibrio_detailed_tsv, - srst2_vibrio_docker = merlin_magic.srst2_vibrio_docker, - srst2_vibrio_database = merlin_magic.srst2_vibrio_database, - srst2_vibrio_version = merlin_magic.srst2_vibrio_version, - srst2_vibrio_ctxA = merlin_magic.srst2_vibrio_ctxA, - srst2_vibrio_ompW = merlin_magic.srst2_vibrio_ompW, - srst2_vibrio_toxR = merlin_magic.srst2_vibrio_toxR, - srst2_vibrio_serogroup = merlin_magic.srst2_vibrio_serogroup, - srst2_vibrio_biotype = merlin_magic.srst2_vibrio_biotype, - abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, - abricate_vibrio_database = merlin_magic.abricate_vibrio_database, - abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, - abricate_vibrio_version = merlin_magic.abricate_vibrio_version, - abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, - abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, - abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, - abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, - abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup, - qc_check = qc_check_task.qc_check, - qc_standard = qc_check_task.qc_standard + read1 = read_QC_trim.read1_clean, + paired_end = false + } + if (defined(taxon_tables)) { + call terra_tools.export_taxon_tables { + input: + terra_project = terra_project, + terra_workspace = terra_workspace, + sample_taxon = gambit.gambit_predicted_taxon, + taxon_tables = taxon_tables, + samplename = samplename, + read1 = read1, + read1_clean = read_QC_trim.read1_clean, + run_id = run_id, + collection_date = collection_date, + originating_lab = originating_lab, + city = city, + county = county, + zip = zip, + theiaprok_illumina_se_version = version_capture.phb_version, + theiaprok_illumina_se_analysis_date = version_capture.date, + seq_platform = seq_method, + num_reads_raw1 = read_QC_trim.fastq_scan_raw1, + fastq_scan_version = read_QC_trim.fastq_scan_version, + num_reads_clean1 = read_QC_trim.fastq_scan_clean1, + trimmomatic_version = read_QC_trim.trimmomatic_version, + fastp_version = read_QC_trim.fastp_version, + bbduk_docker = read_QC_trim.bbduk_docker, + r1_mean_q_raw = cg_pipeline_raw.r1_mean_q, + r1_mean_q_clean = cg_pipeline_clean.r1_mean_q, + r1_mean_readlength_raw = cg_pipeline_raw.r1_mean_readlength, + r1_mean_readlength_clean = cg_pipeline_clean.r1_mean_readlength, + assembly_fasta = shovill_se.assembly_fasta, + contigs_gfa = shovill_se.contigs_gfa, + shovill_se_version = shovill_se.shovill_version, + quast_report = quast.quast_report, + quast_version = quast.version, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + cg_pipeline_report_raw = cg_pipeline_raw.cg_pipeline_report, + cg_pipeline_docker = cg_pipeline_raw.cg_pipeline_docker, + est_coverage_raw = cg_pipeline_raw.est_coverage, + cg_pipeline_report_clean = cg_pipeline_clean.cg_pipeline_report, + est_coverage_clean = cg_pipeline_clean.est_coverage, + gambit_report = gambit.gambit_report_file, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, + gambit_closest_genomes = gambit.gambit_closest_genomes_file, + gambit_version = gambit.gambit_version, + gambit_db_version = gambit.gambit_db_version, + gambit_docker = gambit.gambit_docker, + busco_version = busco.busco_version, + busco_database = busco.busco_database, + busco_results = busco.busco_results, + busco_report = busco.busco_report, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, + ani_output_tsv = ani.ani_output_tsv, + ani_top_species_match = ani.ani_top_species_match, + ani_mummer_version = ani.ani_mummer_version, + ani_docker = ani.ani_docker, + kmerfinder_docker = kmerfinder.kmerfinder_docker, + kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, + kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, + kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, + kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, + kmerfinder_database = kmerfinder.kmerfinder_database, + amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, + amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, + amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, + amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, + amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, + amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, + amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, + amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, + amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, + amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, + amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, + amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, + resfinder_pheno_table = resfinder_task.resfinder_pheno_table, + resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, + resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, + resfinder_results = resfinder_task.resfinder_results_tab, + resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, + resfinder_pointfinder_results = resfinder_task.pointfinder_results, + resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, + resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, + resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, + resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, + resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, + resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, + resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, + resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, + resfinder_db_version = resfinder_task.resfinder_db_version, + resfinder_docker = resfinder_task.resfinder_docker, + ts_mlst_results = ts_mlst.ts_mlst_results, + ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, + ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, + ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, + ts_mlst_version = ts_mlst.ts_mlst_version, + ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, + ts_mlst_docker = ts_mlst.ts_mlst_docker, + serotypefinder_report = merlin_magic.serotypefinder_report, + serotypefinder_docker = merlin_magic.serotypefinder_docker, + serotypefinder_serotype = merlin_magic.serotypefinder_serotype, + ectyper_results = merlin_magic.ectyper_results, + ectyper_version = merlin_magic.ectyper_version, + ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, + shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, + shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, + shigatyper_notes = merlin_magic.shigatyper_notes, + shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, + shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, + shigatyper_version = merlin_magic.shigatyper_version, + shigatyper_docker = merlin_magic.shigatyper_docker, + shigeifinder_report = merlin_magic.shigeifinder_report, + shigeifinder_docker = merlin_magic.shigeifinder_docker, + shigeifinder_version = merlin_magic.shigeifinder_version, + shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, + shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, + shigeifinder_cluster = merlin_magic.shigeifinder_cluster, + shigeifinder_serotype = merlin_magic.shigeifinder_serotype, + shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, + shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, + shigeifinder_notes = merlin_magic.shigeifinder_notes, + shigeifinder_report_reads = merlin_magic.shigeifinder_report_reads, + shigeifinder_docker_reads = merlin_magic.shigeifinder_docker_reads, + shigeifinder_version_reads = merlin_magic.shigeifinder_version_reads, + shigeifinder_ipaH_presence_absence_reads = merlin_magic.shigeifinder_ipaH_presence_absence_reads, + shigeifinder_num_virulence_plasmid_genes_reads = merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, + shigeifinder_cluster_reads = merlin_magic.shigeifinder_cluster_reads, + shigeifinder_serotype_reads = merlin_magic.shigeifinder_serotype_reads, + shigeifinder_O_antigen_reads = merlin_magic.shigeifinder_O_antigen_reads, + shigeifinder_H_antigen_reads = merlin_magic.shigeifinder_H_antigen_reads, + shigeifinder_notes_reads = merlin_magic.shigeifinder_notes_reads, + virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, + virulencefinder_docker = merlin_magic.virulencefinder_docker, + virulencefinder_hits = merlin_magic.virulencefinder_hits, + sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, + sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, + sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, + sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, + sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, + sonneityping_species = merlin_magic.sonneityping_species, + sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, + sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, + sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, + lissero_results = merlin_magic.lissero_results, + lissero_version = merlin_magic.lissero_version, + lissero_serotype = merlin_magic.lissero_serotype, + sistr_results = merlin_magic.sistr_results, + sistr_allele_json = merlin_magic.sistr_allele_json, + sistr_allele_fasta = merlin_magic.sistr_allele_fasta, + sistr_cgmlst = merlin_magic.sistr_cgmlst, + sistr_version = merlin_magic.sistr_version, + sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, + seqsero2_report = merlin_magic.seqsero2_report, + seqsero2_version = merlin_magic.seqsero2_version, + seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, + seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, + seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, + genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, + genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, + genotyphi_version = merlin_magic.genotyphi_version, + genotyphi_species = merlin_magic.genotyphi_species, + genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, + genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, + genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, + kleborate_output_file = merlin_magic.kleborate_output_file, + kleborate_version = merlin_magic.kleborate_version, + kleborate_docker = merlin_magic.kleborate_docker, + kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, + kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, + kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, + kleborate_klocus = merlin_magic.kleborate_klocus, + kleborate_ktype = merlin_magic.kleborate_ktype, + kleborate_olocus = merlin_magic.kleborate_olocus, + kleborate_otype = merlin_magic.kleborate_otype, + kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, + kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, + ngmaster_tsv = merlin_magic.ngmaster_tsv, + ngmaster_version = merlin_magic.ngmaster_version, + ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, + ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, + ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, + ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, + ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, + ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, + ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, + ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, + ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, + ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, + ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, + meningotype_tsv = merlin_magic.meningotype_tsv, + meningotype_version = merlin_magic.meningotype_version, + meningotype_serogroup = merlin_magic.meningotype_serogroup, + meningotype_PorA = merlin_magic.meningotype_PorA, + meningotype_FetA = merlin_magic.meningotype_FetA, + meningotype_PorB = merlin_magic.meningotype_PorB, + meningotype_fHbp = merlin_magic.meningotype_fHbp, + meningotype_NHBA = merlin_magic.meningotype_NHBA, + meningotype_NadA = merlin_magic.meningotype_NadA, + meningotype_BAST = merlin_magic.meningotype_BAST, + kaptive_output_file_k = merlin_magic.kaptive_output_file_k, + kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, + kaptive_version = merlin_magic.kaptive_version, + kaptive_k_locus = merlin_magic.kaptive_k_match, + kaptive_k_type = merlin_magic.kaptive_k_type, + kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, + kaptive_oc_locus = merlin_magic.kaptive_oc_match, + kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, + abricate_results_tsv = abricate.abricate_results, + abricate_genes = abricate.abricate_genes, + abricate_database = abricate.abricate_database, + abricate_version = abricate.abricate_version, + abricate_docker = abricate.abricate_docker, + abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, + abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, + abricate_abaum_database = merlin_magic.abricate_abaum_database, + abricate_abaum_version = merlin_magic.abricate_abaum_version, + abricate_abaum_docker = merlin_magic.abricate_abaum_docker, + tbprofiler_output_file = merlin_magic.tbprofiler_output_file, + tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, + tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, + tbprofiler_version = merlin_magic.tbprofiler_version, + tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, + tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, + tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, + tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, + legsta_results = merlin_magic.legsta_results, + legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, + legsta_version = merlin_magic.legsta_version, + prokka_gff = prokka.prokka_gff, + prokka_gbk = prokka.prokka_gbk, + prokka_sqn = prokka.prokka_sqn, + bakta_gbff = bakta.bakta_gbff, + bakta_gff3 = bakta.bakta_gff3, + bakta_tsv = bakta.bakta_tsv, + bakta_summary = bakta.bakta_txt, + bakta_version = bakta.bakta_version, + plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, + plasmidfinder_results = plasmidfinder.plasmidfinder_results, + plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, + plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, + plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, + pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, + pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, + pbptyper_version = merlin_magic.pbptyper_version, + pbptyper_docker = merlin_magic.pbptyper_docker, + poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, + poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, + poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, + poppunk_version = merlin_magic.poppunk_version, + poppunk_docker = merlin_magic.poppunk_docker, + spatyper_tsv = merlin_magic.spatyper_tsv, + spatyper_docker = merlin_magic.spatyper_docker, + spatyper_repeats = merlin_magic.spatyper_repeats, + spatyper_type = merlin_magic.spatyper_type, + spatyper_version = merlin_magic.spatyper_version, + staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, + staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, + staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, + staphopiasccmec_version = merlin_magic.staphopiasccmec_version, + staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, + agrvate_summary = merlin_magic.agrvate_summary, + agrvate_results = merlin_magic.agrvate_results, + agrvate_agr_group = merlin_magic.agrvate_agr_group, + agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, + agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, + agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, + agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, + agrvate_version = merlin_magic.agrvate_version, + agrvate_docker = merlin_magic.agrvate_docker, + emmtyper_emm_type = merlin_magic.emmtyper_emm_type, + emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, + emmtyper_version = merlin_magic.emmtyper_version, + emmtyper_docker = merlin_magic.emmtyper_docker, + midas_docker = read_QC_trim.midas_docker, + midas_report = read_QC_trim.midas_report, + midas_primary_genus = read_QC_trim.midas_primary_genus, + midas_secondary_genus = read_QC_trim.midas_secondary_genus, + midas_secondary_genus_abundance = read_QC_trim.midas_secondary_genus_abundance, + midas_secondary_genus_coverage = read_QC_trim.midas_secondary_genus_coverage, + kraken2_version = read_QC_trim.kraken_version, + kraken2_docker = read_QC_trim.kraken_docker, + kraken2_report = read_QC_trim.kraken_report, + pasty_serogroup = merlin_magic.pasty_serogroup, + pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, + pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, + pasty_summary_tsv = merlin_magic.pasty_summary_tsv, + pasty_blast_hits = merlin_magic.pasty_blast_hits, + pasty_all_serogroups = merlin_magic.pasty_all_serogroups, + pasty_version = merlin_magic.pasty_version, + pasty_docker = merlin_magic.pasty_docker, + pasty_comment = merlin_magic.pasty_comment, + hicap_serotype = merlin_magic.hicap_serotype, + hicap_genes = merlin_magic.hicap_genes, + hicap_results_tsv = merlin_magic.hicap_results_tsv, + hicap_version = merlin_magic.hicap_version, + hicap_docker = merlin_magic.hicap_docker, + srst2_vibrio_detailed_tsv = merlin_magic.srst2_vibrio_detailed_tsv, + srst2_vibrio_docker = merlin_magic.srst2_vibrio_docker, + srst2_vibrio_database = merlin_magic.srst2_vibrio_database, + srst2_vibrio_version = merlin_magic.srst2_vibrio_version, + srst2_vibrio_ctxA = merlin_magic.srst2_vibrio_ctxA, + srst2_vibrio_ompW = merlin_magic.srst2_vibrio_ompW, + srst2_vibrio_toxR = merlin_magic.srst2_vibrio_toxR, + srst2_vibrio_serogroup = merlin_magic.srst2_vibrio_serogroup, + srst2_vibrio_biotype = merlin_magic.srst2_vibrio_biotype, + abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, + abricate_vibrio_database = merlin_magic.abricate_vibrio_database, + abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, + abricate_vibrio_version = merlin_magic.abricate_vibrio_version, + abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, + abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, + abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, + abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, + abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup, + qc_check = qc_check_task.qc_check, + qc_standard = qc_check_task.qc_standard + } } } } diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index bfbc26aea..742c21191 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -49,6 +49,7 @@ workflow theiaprok_ont { Int max_genome_length = 18040666 Int min_coverage = 5 # reduced from 10 because some institutions sequence at lower depth because of longer read length # module options + Boolean perform_characterization = true # by default run all characterization steps Boolean call_ani = false # by default do not call ANI task, but user has ability to enable this task if working with enteric pathogens or supply their own high-quality reference genome Boolean call_kmerfinder = false Boolean call_resfinder = false @@ -130,415 +131,418 @@ workflow theiaprok_ont { assembly = dragonflye.assembly_fasta, samplename = samplename } - if (call_ani) { - call ani_task.animummer as ani { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename + if (perform_characterization) { + + if (call_ani) { + call ani_task.animummer as ani { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } } - } - if (call_kmerfinder) { - call kmerfinder_task.kmerfinder_bacteria as kmerfinder { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename + if (call_kmerfinder) { + call kmerfinder_task.kmerfinder_bacteria as kmerfinder { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } } - } - call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename, - organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) - } - if (call_resfinder) { - call resfinder_task.resfinder as resfinder_task { + call amrfinderplus.amrfinderplus_nuc as amrfinderplus_task { input: assembly = dragonflye.assembly_fasta, samplename = samplename, organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) } - } - call ts_mlst_task.ts_mlst { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename - } - if (genome_annotation == "prokka") { - call prokka_task.prokka { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename + if (call_resfinder) { + call resfinder_task.resfinder as resfinder_task { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename, + organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) + } } - } - if (genome_annotation == "bakta") { - call bakta_task.bakta { - input: + call ts_mlst_task.ts_mlst { + input: assembly = dragonflye.assembly_fasta, samplename = samplename } - } - if (call_plasmidfinder) { - call plasmidfinder_task.plasmidfinder { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename + if (genome_annotation == "prokka") { + call prokka_task.prokka { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } } - } - if (call_abricate) { - call abricate_task.abricate { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename, - database = abricate_db + if (genome_annotation == "bakta") { + call bakta_task.bakta { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } } - } - if (defined(qc_check_table)) { - call qc_check.qc_check_phb as qc_check_task { - input: - qc_check_table = qc_check_table, - expected_taxon = expected_taxon, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - num_reads_raw1 = nanoplot_raw.num_reads, - num_reads_clean1 = nanoplot_clean.num_reads, - r1_mean_q_raw = nanoplot_raw.mean_q, - r1_mean_readlength_raw = nanoplot_raw.mean_readlength, - r1_mean_q_clean = nanoplot_clean.mean_q, - r1_mean_readlength_clean = nanoplot_clean.mean_readlength, - est_coverage_raw = nanoplot_raw.est_coverage, - est_coverage_clean = nanoplot_clean.est_coverage, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - busco_results = busco.busco_results, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + if (call_plasmidfinder) { + call plasmidfinder_task.plasmidfinder { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } } - } - call merlin_magic_workflow.merlin_magic { - input: - merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), - assembly = dragonflye.assembly_fasta, - samplename = samplename, - read1 = read_qc_trim.read1_clean, - ont_data = true - } - if (defined(taxon_tables)) { - call terra_tools_task.export_taxon_tables { + if (call_abricate) { + call abricate_task.abricate { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename, + database = abricate_db + } + } + if (defined(qc_check_table)) { + call qc_check.qc_check_phb as qc_check_task { + input: + qc_check_table = qc_check_table, + expected_taxon = expected_taxon, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + num_reads_raw1 = nanoplot_raw.num_reads, + num_reads_clean1 = nanoplot_clean.num_reads, + r1_mean_q_raw = nanoplot_raw.mean_q, + r1_mean_readlength_raw = nanoplot_raw.mean_readlength, + r1_mean_q_clean = nanoplot_clean.mean_q, + r1_mean_readlength_clean = nanoplot_clean.mean_readlength, + est_coverage_raw = nanoplot_raw.est_coverage, + est_coverage_clean = nanoplot_clean.est_coverage, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + busco_results = busco.busco_results, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned + } + } + call merlin_magic_workflow.merlin_magic { input: - terra_project = terra_project, - terra_workspace = terra_workspace, - sample_taxon = gambit.gambit_predicted_taxon, - taxon_tables = taxon_tables, + merlin_tag = select_first([expected_taxon, gambit.merlin_tag]), + assembly = dragonflye.assembly_fasta, samplename = samplename, - read1 = read1, - read1_clean = read_qc_trim.read1_clean, - run_id = run_id, - collection_date = collection_date, - originating_lab = originating_lab, - city = city, - county = county, - zip = zip, - theiaprok_ont_version = version_capture.phb_version, - theiaprok_ont_analysis_date = version_capture.date, - seq_platform = seq_method, - num_reads_raw1 = nanoplot_raw.num_reads, - num_reads_clean1 = nanoplot_clean.num_reads, - r1_mean_q_raw = nanoplot_clean.mean_q, - r1_mean_q_clean = nanoplot_clean.mean_q, - r1_mean_readlength_raw = nanoplot_raw.mean_readlength, - r1_mean_readlength_clean = nanoplot_clean.mean_readlength, - nanoq_version = read_qc_trim.nanoq_version, - nanoplot_version = nanoplot_raw.nanoplot_version, - nanoplot_docker = nanoplot_raw.nanoplot_docker, - nanoplot_html_raw = nanoplot_raw.nanoplot_html, - nanoplot_tsv_raw = nanoplot_raw.nanoplot_tsv, - nanoplot_num_reads_raw1 = nanoplot_raw.num_reads, - nanoplot_r1_median_readlength_raw = nanoplot_raw.median_readlength, - nanoplot_r1_mean_readlength_raw = nanoplot_raw.mean_readlength, - nanoplot_r1_stdev_readlength_raw = nanoplot_raw.stdev_readlength, - nanoplot_r1_n50_raw = nanoplot_raw.n50, - nanoplot_r1_mean_q_raw = nanoplot_raw.mean_q, - nanoplot_r1_median_q_raw = nanoplot_raw.median_q, - nanoplot_r1_est_coverage_raw = nanoplot_raw.est_coverage, - nanoplot_html_clean = nanoplot_clean.nanoplot_html, - nanoplot_tsv_clean = nanoplot_clean.nanoplot_tsv, - nanoplot_num_reads_clean1 = nanoplot_clean.num_reads, - nanoplot_r1_median_readlength_clean = nanoplot_clean.median_readlength, - nanoplot_r1_mean_readlength_clean = nanoplot_clean.mean_readlength, - nanoplot_r1_stdev_readlength_clean = nanoplot_clean.stdev_readlength, - nanoplot_r1_n50_clean = nanoplot_clean.n50, - nanoplot_r1_mean_q_clean = nanoplot_clean.mean_q, - nanoplot_r1_median_q_clean = nanoplot_clean.median_q, - nanoplot_r1_est_coverage_clean = nanoplot_clean.est_coverage, - kmc_est_genome_length = read_qc_trim.est_genome_length, - kmc_kmer_stats = read_qc_trim.kmc_kmer_stats, - kmc_version = read_qc_trim.kmc_version, - rasusa_version = read_qc_trim.rasusa_version, - tiptoft_plasmid_replicon_fastq = read_qc_trim.tiptoft_plasmid_replicon_fastq, - tiptoft_plasmid_replicon_genes = read_qc_trim.tiptoft_plasmid_replicon_genes, - tiptoft_version = read_qc_trim.tiptoft_version, - assembly_fasta = dragonflye.assembly_fasta, - contigs_gfa = dragonflye.contigs_gfa, - dragonflye_version = dragonflye.dragonflye_version, - quast_report = quast.quast_report, - quast_version = quast.version, - assembly_length = quast.genome_length, - number_contigs = quast.number_contigs, - n50_value = quast.n50_value, - quast_gc_percent = quast.gc_percent, - est_coverage_raw = nanoplot_raw.est_coverage, - est_coverage_clean = nanoplot_clean.est_coverage, - gambit_report = gambit.gambit_report_file, - gambit_predicted_taxon = gambit.gambit_predicted_taxon, - gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, - gambit_closest_genomes = gambit.gambit_closest_genomes_file, - gambit_version = gambit.gambit_version, - gambit_db_version = gambit.gambit_db_version, - gambit_docker = gambit.gambit_docker, - busco_version = busco.busco_version, - busco_database = busco.busco_database, - busco_results = busco.busco_results, - busco_report = busco.busco_report, - ani_highest_percent = ani.ani_highest_percent, - ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, - ani_output_tsv = ani.ani_output_tsv, - ani_top_species_match = ani.ani_top_species_match, - ani_mummer_version = ani.ani_mummer_version, - ani_docker = ani.ani_docker, - kmerfinder_docker = kmerfinder.kmerfinder_docker, - kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, - kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, - kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, - kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, - kmerfinder_database = kmerfinder.kmerfinder_database, - amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, - amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, - amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, - amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, - amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, - amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, - amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, - amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, - amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, - amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, - amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, - amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, - resfinder_pheno_table = resfinder_task.resfinder_pheno_table, - resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, - resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, - resfinder_results = resfinder_task.resfinder_results_tab, - resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, - resfinder_pointfinder_results = resfinder_task.pointfinder_results, - resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, - resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, - resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, - resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, - resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, - resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, - resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, - resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, - resfinder_db_version = resfinder_task.resfinder_db_version, - resfinder_docker = resfinder_task.resfinder_docker, - ts_mlst_results = ts_mlst.ts_mlst_results, - ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, - ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, - ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, - ts_mlst_version = ts_mlst.ts_mlst_version, - ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, - ts_mlst_docker = ts_mlst.ts_mlst_docker, - serotypefinder_report = merlin_magic.serotypefinder_report, - serotypefinder_docker = merlin_magic.serotypefinder_docker, - serotypefinder_serotype = merlin_magic.serotypefinder_serotype, - ectyper_results = merlin_magic.ectyper_results, - ectyper_version = merlin_magic.ectyper_version, - ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, - shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, - shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, - shigatyper_notes = merlin_magic.shigatyper_notes, - shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, - shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, - shigatyper_version = merlin_magic.shigatyper_version, - shigatyper_docker = merlin_magic.shigatyper_docker, - shigeifinder_report = merlin_magic.shigeifinder_report, - shigeifinder_docker = merlin_magic.shigeifinder_docker, - shigeifinder_version = merlin_magic.shigeifinder_version, - shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, - shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, - shigeifinder_cluster = merlin_magic.shigeifinder_cluster, - shigeifinder_serotype = merlin_magic.shigeifinder_serotype, - shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, - shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, - shigeifinder_notes = merlin_magic.shigeifinder_notes, - virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, - virulencefinder_docker = merlin_magic.virulencefinder_docker, - virulencefinder_hits = merlin_magic.virulencefinder_hits, - sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, - sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, - sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, - sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, - sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, - sonneityping_species = merlin_magic.sonneityping_species, - sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, - sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, - sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, - lissero_results = merlin_magic.lissero_results, - lissero_version = merlin_magic.lissero_version, - lissero_serotype = merlin_magic.lissero_serotype, - sistr_results = merlin_magic.sistr_results, - sistr_allele_json = merlin_magic.sistr_allele_json, - sistr_allele_fasta = merlin_magic.sistr_allele_fasta, - sistr_cgmlst = merlin_magic.sistr_cgmlst, - sistr_version = merlin_magic.sistr_version, - sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, - seqsero2_report = merlin_magic.seqsero2_report, - seqsero2_version = merlin_magic.seqsero2_version, - seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, - seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, - seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, - genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, - genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, - genotyphi_version = merlin_magic.genotyphi_version, - genotyphi_species = merlin_magic.genotyphi_species, - genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, - genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, - genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, - kleborate_output_file = merlin_magic.kleborate_output_file, - kleborate_version = merlin_magic.kleborate_version, - kleborate_docker = merlin_magic.kleborate_docker, - kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, - kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, - kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, - kleborate_klocus = merlin_magic.kleborate_klocus, - kleborate_ktype = merlin_magic.kleborate_ktype, - kleborate_olocus = merlin_magic.kleborate_olocus, - kleborate_otype = merlin_magic.kleborate_otype, - kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, - kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, - kleborate_virulence_score = merlin_magic.kleborate_virulence_score, - kleborate_resistance_score = merlin_magic.kleborate_resistance_score, - ngmaster_tsv = merlin_magic.ngmaster_tsv, - ngmaster_version = merlin_magic.ngmaster_version, - ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, - ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, - ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, - ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, - ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, - ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, - ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, - ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, - ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, - ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, - ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, - meningotype_tsv = merlin_magic.meningotype_tsv, - meningotype_version = merlin_magic.meningotype_version, - meningotype_serogroup = merlin_magic.meningotype_serogroup, - meningotype_PorA = merlin_magic.meningotype_PorA, - meningotype_FetA = merlin_magic.meningotype_FetA, - meningotype_PorB = merlin_magic.meningotype_PorB, - meningotype_fHbp = merlin_magic.meningotype_fHbp, - meningotype_NHBA = merlin_magic.meningotype_NHBA, - meningotype_NadA = merlin_magic.meningotype_NadA, - meningotype_BAST = merlin_magic.meningotype_BAST, - kaptive_output_file_k = merlin_magic.kaptive_output_file_k, - kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, - kaptive_version = merlin_magic.kaptive_version, - kaptive_k_locus = merlin_magic.kaptive_k_match, - kaptive_k_type = merlin_magic.kaptive_k_type, - kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, - kaptive_oc_locus = merlin_magic.kaptive_oc_match, - kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, - abricate_results_tsv = abricate.abricate_results, - abricate_genes = abricate.abricate_genes, - abricate_database = abricate.abricate_database, - abricate_version = abricate.abricate_version, - abricate_docker = abricate.abricate_docker, - abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, - abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, - abricate_abaum_database = merlin_magic.abricate_abaum_database, - abricate_abaum_version = merlin_magic.abricate_abaum_version, - abricate_abaum_docker = merlin_magic.abricate_abaum_docker, - tbprofiler_output_file = merlin_magic.tbprofiler_output_file, - tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, - tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, - tbprofiler_version = merlin_magic.tbprofiler_version, - tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, - tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, - tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, - tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, - legsta_results = merlin_magic.legsta_results, - legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, - legsta_version = merlin_magic.legsta_version, - prokka_gff = prokka.prokka_gff, - prokka_gbk = prokka.prokka_gbk, - prokka_sqn = prokka.prokka_sqn, - bakta_gbff = bakta.bakta_gbff, - bakta_gff3 = bakta.bakta_gff3, - bakta_tsv = bakta.bakta_tsv, - bakta_summary = bakta.bakta_txt, - bakta_version = bakta.bakta_version, - plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, - plasmidfinder_results = plasmidfinder.plasmidfinder_results, - plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, - plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, - plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, - pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, - pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, - pbptyper_version = merlin_magic.pbptyper_version, - pbptyper_docker = merlin_magic.pbptyper_docker, - poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, - poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, - poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, - poppunk_version = merlin_magic.poppunk_version, - poppunk_docker = merlin_magic.poppunk_docker, - spatyper_tsv = merlin_magic.spatyper_tsv, - spatyper_docker = merlin_magic.spatyper_docker, - spatyper_repeats = merlin_magic.spatyper_repeats, - spatyper_type = merlin_magic.spatyper_type, - spatyper_version = merlin_magic.spatyper_version, - staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, - staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, - staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, - staphopiasccmec_version = merlin_magic.staphopiasccmec_version, - staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, - agrvate_summary = merlin_magic.agrvate_summary, - agrvate_results = merlin_magic.agrvate_results, - agrvate_agr_group = merlin_magic.agrvate_agr_group, - agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, - agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, - agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, - agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, - agrvate_version = merlin_magic.agrvate_version, - agrvate_docker = merlin_magic.agrvate_docker, - emmtyper_emm_type = merlin_magic.emmtyper_emm_type, - emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, - emmtyper_version = merlin_magic.emmtyper_version, - emmtyper_docker = merlin_magic.emmtyper_docker, - pasty_serogroup = merlin_magic.pasty_serogroup, - pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, - pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, - pasty_summary_tsv = merlin_magic.pasty_summary_tsv, - pasty_blast_hits = merlin_magic.pasty_blast_hits, - pasty_all_serogroups = merlin_magic.pasty_all_serogroups, - pasty_version = merlin_magic.pasty_version, - pasty_docker = merlin_magic.pasty_docker, - pasty_comment = merlin_magic.pasty_comment, - qc_check = qc_check_task.qc_check, - qc_standard = qc_check_task.qc_standard, - hicap_serotype = merlin_magic.hicap_serotype, - hicap_genes = merlin_magic.hicap_genes, - hicap_results_tsv = merlin_magic.hicap_results_tsv, - hicap_version = merlin_magic.hicap_version, - hicap_docker = merlin_magic.hicap_docker, - abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, - abricate_vibrio_database = merlin_magic.abricate_vibrio_database, - abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, - abricate_vibrio_version = merlin_magic.abricate_vibrio_version, - abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, - abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, - abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, - abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, - abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + read1 = read_qc_trim.read1_clean, + ont_data = true + } + if (defined(taxon_tables)) { + call terra_tools_task.export_taxon_tables { + input: + terra_project = terra_project, + terra_workspace = terra_workspace, + sample_taxon = gambit.gambit_predicted_taxon, + taxon_tables = taxon_tables, + samplename = samplename, + read1 = read1, + read1_clean = read_qc_trim.read1_clean, + run_id = run_id, + collection_date = collection_date, + originating_lab = originating_lab, + city = city, + county = county, + zip = zip, + theiaprok_ont_version = version_capture.phb_version, + theiaprok_ont_analysis_date = version_capture.date, + seq_platform = seq_method, + num_reads_raw1 = nanoplot_raw.num_reads, + num_reads_clean1 = nanoplot_clean.num_reads, + r1_mean_q_raw = nanoplot_clean.mean_q, + r1_mean_q_clean = nanoplot_clean.mean_q, + r1_mean_readlength_raw = nanoplot_raw.mean_readlength, + r1_mean_readlength_clean = nanoplot_clean.mean_readlength, + nanoq_version = read_qc_trim.nanoq_version, + nanoplot_version = nanoplot_raw.nanoplot_version, + nanoplot_docker = nanoplot_raw.nanoplot_docker, + nanoplot_html_raw = nanoplot_raw.nanoplot_html, + nanoplot_tsv_raw = nanoplot_raw.nanoplot_tsv, + nanoplot_num_reads_raw1 = nanoplot_raw.num_reads, + nanoplot_r1_median_readlength_raw = nanoplot_raw.median_readlength, + nanoplot_r1_mean_readlength_raw = nanoplot_raw.mean_readlength, + nanoplot_r1_stdev_readlength_raw = nanoplot_raw.stdev_readlength, + nanoplot_r1_n50_raw = nanoplot_raw.n50, + nanoplot_r1_mean_q_raw = nanoplot_raw.mean_q, + nanoplot_r1_median_q_raw = nanoplot_raw.median_q, + nanoplot_r1_est_coverage_raw = nanoplot_raw.est_coverage, + nanoplot_html_clean = nanoplot_clean.nanoplot_html, + nanoplot_tsv_clean = nanoplot_clean.nanoplot_tsv, + nanoplot_num_reads_clean1 = nanoplot_clean.num_reads, + nanoplot_r1_median_readlength_clean = nanoplot_clean.median_readlength, + nanoplot_r1_mean_readlength_clean = nanoplot_clean.mean_readlength, + nanoplot_r1_stdev_readlength_clean = nanoplot_clean.stdev_readlength, + nanoplot_r1_n50_clean = nanoplot_clean.n50, + nanoplot_r1_mean_q_clean = nanoplot_clean.mean_q, + nanoplot_r1_median_q_clean = nanoplot_clean.median_q, + nanoplot_r1_est_coverage_clean = nanoplot_clean.est_coverage, + kmc_est_genome_length = read_qc_trim.est_genome_length, + kmc_kmer_stats = read_qc_trim.kmc_kmer_stats, + kmc_version = read_qc_trim.kmc_version, + rasusa_version = read_qc_trim.rasusa_version, + tiptoft_plasmid_replicon_fastq = read_qc_trim.tiptoft_plasmid_replicon_fastq, + tiptoft_plasmid_replicon_genes = read_qc_trim.tiptoft_plasmid_replicon_genes, + tiptoft_version = read_qc_trim.tiptoft_version, + assembly_fasta = dragonflye.assembly_fasta, + contigs_gfa = dragonflye.contigs_gfa, + dragonflye_version = dragonflye.dragonflye_version, + quast_report = quast.quast_report, + quast_version = quast.version, + assembly_length = quast.genome_length, + number_contigs = quast.number_contigs, + n50_value = quast.n50_value, + quast_gc_percent = quast.gc_percent, + est_coverage_raw = nanoplot_raw.est_coverage, + est_coverage_clean = nanoplot_clean.est_coverage, + gambit_report = gambit.gambit_report_file, + gambit_predicted_taxon = gambit.gambit_predicted_taxon, + gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank, + gambit_closest_genomes = gambit.gambit_closest_genomes_file, + gambit_version = gambit.gambit_version, + gambit_db_version = gambit.gambit_db_version, + gambit_docker = gambit.gambit_docker, + busco_version = busco.busco_version, + busco_database = busco.busco_database, + busco_results = busco.busco_results, + busco_report = busco.busco_report, + ani_highest_percent = ani.ani_highest_percent, + ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned, + ani_output_tsv = ani.ani_output_tsv, + ani_top_species_match = ani.ani_top_species_match, + ani_mummer_version = ani.ani_mummer_version, + ani_docker = ani.ani_docker, + kmerfinder_docker = kmerfinder.kmerfinder_docker, + kmerfinder_results_tsv = kmerfinder.kmerfinder_results_tsv, + kmerfinder_top_hit = kmerfinder.kmerfinder_top_hit, + kmerfinder_query_coverage = kmerfinder.kmerfinder_query_coverage, + kmerfinder_template_coverage = kmerfinder.kmerfinder_template_coverage, + kmerfinder_database = kmerfinder.kmerfinder_database, + amrfinderplus_all_report = amrfinderplus_task.amrfinderplus_all_report, + amrfinderplus_amr_report = amrfinderplus_task.amrfinderplus_amr_report, + amrfinderplus_stress_report = amrfinderplus_task.amrfinderplus_stress_report, + amrfinderplus_virulence_report = amrfinderplus_task.amrfinderplus_virulence_report, + amrfinderplus_amr_core_genes = amrfinderplus_task.amrfinderplus_amr_core_genes, + amrfinderplus_amr_plus_genes = amrfinderplus_task.amrfinderplus_amr_plus_genes, + amrfinderplus_stress_genes = amrfinderplus_task.amrfinderplus_stress_genes, + amrfinderplus_virulence_genes = amrfinderplus_task.amrfinderplus_virulence_genes, + amrfinderplus_amr_classes = amrfinderplus_task.amrfinderplus_amr_classes, + amrfinderplus_amr_subclasses = amrfinderplus_task.amrfinderplus_amr_subclasses, + amrfinderplus_version = amrfinderplus_task.amrfinderplus_version, + amrfinderplus_db_version = amrfinderplus_task.amrfinderplus_db_version, + resfinder_pheno_table = resfinder_task.resfinder_pheno_table, + resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species, + resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq, + resfinder_results = resfinder_task.resfinder_results_tab, + resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, + resfinder_pointfinder_results = resfinder_task.pointfinder_results, + resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, + resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, + resfinder_predicted_resistance_Amp = resfinder_task.resfinder_predicted_resistance_Amp, + resfinder_predicted_resistance_Azm = resfinder_task.resfinder_predicted_resistance_Azm, + resfinder_predicted_resistance_Axo = resfinder_task.resfinder_predicted_resistance_Axo, + resfinder_predicted_resistance_Cip = resfinder_task.resfinder_predicted_resistance_Cip, + resfinder_predicted_resistance_Smx = resfinder_task.resfinder_predicted_resistance_Smx, + resfinder_predicted_resistance_Tmp = resfinder_task.resfinder_predicted_resistance_Tmp, + resfinder_db_version = resfinder_task.resfinder_db_version, + resfinder_docker = resfinder_task.resfinder_docker, + ts_mlst_results = ts_mlst.ts_mlst_results, + ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st, + ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme, + ts_mlst_allelic_profile = ts_mlst.ts_mlst_allelic_profile, + ts_mlst_version = ts_mlst.ts_mlst_version, + ts_mlst_novel_alleles = ts_mlst.ts_mlst_novel_alleles, + ts_mlst_docker = ts_mlst.ts_mlst_docker, + serotypefinder_report = merlin_magic.serotypefinder_report, + serotypefinder_docker = merlin_magic.serotypefinder_docker, + serotypefinder_serotype = merlin_magic.serotypefinder_serotype, + ectyper_results = merlin_magic.ectyper_results, + ectyper_version = merlin_magic.ectyper_version, + ectyper_predicted_serotype = merlin_magic.ectyper_predicted_serotype, + shigatyper_predicted_serotype = merlin_magic.shigatyper_predicted_serotype, + shigatyper_ipaB_presence_absence = merlin_magic.shigatyper_ipaB_presence_absence, + shigatyper_notes = merlin_magic.shigatyper_notes, + shigatyper_hits_tsv = merlin_magic.shigatyper_hits_tsv, + shigatyper_summary_tsv = merlin_magic.shigatyper_summary_tsv, + shigatyper_version = merlin_magic.shigatyper_version, + shigatyper_docker = merlin_magic.shigatyper_docker, + shigeifinder_report = merlin_magic.shigeifinder_report, + shigeifinder_docker = merlin_magic.shigeifinder_docker, + shigeifinder_version = merlin_magic.shigeifinder_version, + shigeifinder_ipaH_presence_absence = merlin_magic.shigeifinder_ipaH_presence_absence, + shigeifinder_num_virulence_plasmid_genes = merlin_magic.shigeifinder_num_virulence_plasmid_genes, + shigeifinder_cluster = merlin_magic.shigeifinder_cluster, + shigeifinder_serotype = merlin_magic.shigeifinder_serotype, + shigeifinder_O_antigen = merlin_magic.shigeifinder_O_antigen, + shigeifinder_H_antigen = merlin_magic.shigeifinder_H_antigen, + shigeifinder_notes = merlin_magic.shigeifinder_notes, + virulencefinder_report_tsv = merlin_magic.virulencefinder_report_tsv, + virulencefinder_docker = merlin_magic.virulencefinder_docker, + virulencefinder_hits = merlin_magic.virulencefinder_hits, + sonneityping_mykrobe_report_csv = merlin_magic.sonneityping_mykrobe_report_csv, + sonneityping_mykrobe_report_json = merlin_magic.sonneityping_mykrobe_report_json, + sonneityping_final_report_tsv = merlin_magic.sonneityping_final_report_tsv, + sonneityping_mykrobe_version = merlin_magic.sonneityping_mykrobe_version, + sonneityping_mykrobe_docker = merlin_magic.sonneityping_mykrobe_docker, + sonneityping_species = merlin_magic.sonneityping_species, + sonneityping_final_genotype = merlin_magic.sonneityping_final_genotype, + sonneityping_genotype_confidence = merlin_magic.sonneityping_genotype_confidence, + sonneityping_genotype_name = merlin_magic.sonneityping_genotype_name, + lissero_results = merlin_magic.lissero_results, + lissero_version = merlin_magic.lissero_version, + lissero_serotype = merlin_magic.lissero_serotype, + sistr_results = merlin_magic.sistr_results, + sistr_allele_json = merlin_magic.sistr_allele_json, + sistr_allele_fasta = merlin_magic.sistr_allele_fasta, + sistr_cgmlst = merlin_magic.sistr_cgmlst, + sistr_version = merlin_magic.sistr_version, + sistr_predicted_serotype = merlin_magic.sistr_predicted_serotype, + seqsero2_report = merlin_magic.seqsero2_report, + seqsero2_version = merlin_magic.seqsero2_version, + seqsero2_predicted_antigenic_profile = merlin_magic.seqsero2_predicted_antigenic_profile, + seqsero2_predicted_serotype = merlin_magic.seqsero2_predicted_serotype, + seqsero2_predicted_contamination = merlin_magic.seqsero2_predicted_contamination, + genotyphi_report_tsv = merlin_magic.genotyphi_report_tsv, + genotyphi_mykrobe_json = merlin_magic.genotyphi_mykrobe_json, + genotyphi_version = merlin_magic.genotyphi_version, + genotyphi_species = merlin_magic.genotyphi_species, + genotyphi_st_probes_percent_coverage = merlin_magic.genotyphi_st_probes_percent_coverage, + genotyphi_final_genotype = merlin_magic.genotyphi_final_genotype, + genotyphi_genotype_confidence = merlin_magic.genotyphi_genotype_confidence, + kleborate_output_file = merlin_magic.kleborate_output_file, + kleborate_version = merlin_magic.kleborate_version, + kleborate_docker = merlin_magic.kleborate_docker, + kleborate_key_resistance_genes = merlin_magic.kleborate_key_resistance_genes, + kleborate_genomic_resistance_mutations = merlin_magic.kleborate_genomic_resistance_mutations, + kleborate_mlst_sequence_type = merlin_magic.kleborate_mlst_sequence_type, + kleborate_klocus = merlin_magic.kleborate_klocus, + kleborate_ktype = merlin_magic.kleborate_ktype, + kleborate_olocus = merlin_magic.kleborate_olocus, + kleborate_otype = merlin_magic.kleborate_otype, + kleborate_klocus_confidence = merlin_magic.kleborate_klocus_confidence, + kleborate_olocus_confidence = merlin_magic.kleborate_olocus_confidence, + kleborate_virulence_score = merlin_magic.kleborate_virulence_score, + kleborate_resistance_score = merlin_magic.kleborate_resistance_score, + ngmaster_tsv = merlin_magic.ngmaster_tsv, + ngmaster_version = merlin_magic.ngmaster_version, + ngmaster_ngmast_sequence_type = merlin_magic.ngmaster_ngmast_sequence_type, + ngmaster_ngmast_porB_allele = merlin_magic.ngmaster_ngmast_porB_allele, + ngmaster_ngmast_tbpB_allele = merlin_magic.ngmaster_ngmast_tbpB_allele, + ngmaster_ngstar_sequence_type = merlin_magic.ngmaster_ngstar_sequence_type, + ngmaster_ngstar_penA_allele = merlin_magic.ngmaster_ngstar_penA_allele, + ngmaster_ngstar_mtrR_allele = merlin_magic.ngmaster_ngstar_mtrR_allele, + ngmaster_ngstar_porB_allele = merlin_magic.ngmaster_ngstar_porB_allele, + ngmaster_ngstar_ponA_allele = merlin_magic.ngmaster_ngstar_ponA_allele, + ngmaster_ngstar_gyrA_allele = merlin_magic.ngmaster_ngstar_gyrA_allele, + ngmaster_ngstar_parC_allele = merlin_magic.ngmaster_ngstar_parC_allele, + ngmaster_ngstar_23S_allele = merlin_magic.ngmaster_ngstar_23S_allele, + meningotype_tsv = merlin_magic.meningotype_tsv, + meningotype_version = merlin_magic.meningotype_version, + meningotype_serogroup = merlin_magic.meningotype_serogroup, + meningotype_PorA = merlin_magic.meningotype_PorA, + meningotype_FetA = merlin_magic.meningotype_FetA, + meningotype_PorB = merlin_magic.meningotype_PorB, + meningotype_fHbp = merlin_magic.meningotype_fHbp, + meningotype_NHBA = merlin_magic.meningotype_NHBA, + meningotype_NadA = merlin_magic.meningotype_NadA, + meningotype_BAST = merlin_magic.meningotype_BAST, + kaptive_output_file_k = merlin_magic.kaptive_output_file_k, + kaptive_output_file_oc = merlin_magic.kaptive_output_file_oc, + kaptive_version = merlin_magic.kaptive_version, + kaptive_k_locus = merlin_magic.kaptive_k_match, + kaptive_k_type = merlin_magic.kaptive_k_type, + kaptive_kl_confidence = merlin_magic.kaptive_k_confidence, + kaptive_oc_locus = merlin_magic.kaptive_oc_match, + kaptive_ocl_confidence = merlin_magic.kaptive_oc_confidence, + abricate_results_tsv = abricate.abricate_results, + abricate_genes = abricate.abricate_genes, + abricate_database = abricate.abricate_database, + abricate_version = abricate.abricate_version, + abricate_docker = abricate.abricate_docker, + abricate_abaum_plasmid_tsv = merlin_magic.abricate_abaum_results, + abricate_abaum_plasmid_type_genes = merlin_magic.abricate_abaum_genes, + abricate_abaum_database = merlin_magic.abricate_abaum_database, + abricate_abaum_version = merlin_magic.abricate_abaum_version, + abricate_abaum_docker = merlin_magic.abricate_abaum_docker, + tbprofiler_output_file = merlin_magic.tbprofiler_output_file, + tbprofiler_output_bam = merlin_magic.tbprofiler_output_bam, + tbprofiler_output_bai = merlin_magic.tbprofiler_output_bai, + tbprofiler_version = merlin_magic.tbprofiler_version, + tbprofiler_main_lineage = merlin_magic.tbprofiler_main_lineage, + tbprofiler_sub_lineage = merlin_magic.tbprofiler_sub_lineage, + tbprofiler_dr_type = merlin_magic.tbprofiler_dr_type, + tbprofiler_resistance_genes = merlin_magic.tbprofiler_resistance_genes, + legsta_results = merlin_magic.legsta_results, + legsta_predicted_sbt = merlin_magic.legsta_predicted_sbt, + legsta_version = merlin_magic.legsta_version, + prokka_gff = prokka.prokka_gff, + prokka_gbk = prokka.prokka_gbk, + prokka_sqn = prokka.prokka_sqn, + bakta_gbff = bakta.bakta_gbff, + bakta_gff3 = bakta.bakta_gff3, + bakta_tsv = bakta.bakta_tsv, + bakta_summary = bakta.bakta_txt, + bakta_version = bakta.bakta_version, + plasmidfinder_plasmids = plasmidfinder.plasmidfinder_plasmids, + plasmidfinder_results = plasmidfinder.plasmidfinder_results, + plasmidfinder_seqs = plasmidfinder.plasmidfinder_seqs, + plasmidfinder_docker = plasmidfinder.plasmidfinder_docker, + plasmidfinder_db_version = plasmidfinder.plasmidfinder_db_version, + pbptyper_predicted_1A_2B_2X = merlin_magic.pbptyper_predicted_1A_2B_2X, + pbptyper_pbptype_predicted_tsv = merlin_magic.pbptyper_pbptype_predicted_tsv, + pbptyper_version = merlin_magic.pbptyper_version, + pbptyper_docker = merlin_magic.pbptyper_docker, + poppunk_gps_cluster = merlin_magic.poppunk_gps_cluster, + poppunk_gps_external_cluster_csv = merlin_magic.poppunk_gps_external_cluster_csv, + poppunk_GPS_db_version = merlin_magic.poppunk_GPS_db_version, + poppunk_version = merlin_magic.poppunk_version, + poppunk_docker = merlin_magic.poppunk_docker, + spatyper_tsv = merlin_magic.spatyper_tsv, + spatyper_docker = merlin_magic.spatyper_docker, + spatyper_repeats = merlin_magic.spatyper_repeats, + spatyper_type = merlin_magic.spatyper_type, + spatyper_version = merlin_magic.spatyper_version, + staphopiasccmec_results_tsv = merlin_magic.staphopiasccmec_results_tsv, + staphopiasccmec_hamming_distance_tsv = merlin_magic.staphopiasccmec_hamming_distance_tsv, + staphopiasccmec_types_and_mecA_presence = merlin_magic.staphopiasccmec_types_and_mecA_presence, + staphopiasccmec_version = merlin_magic.staphopiasccmec_version, + staphopiasccmec_docker = merlin_magic.staphopiasccmec_docker, + agrvate_summary = merlin_magic.agrvate_summary, + agrvate_results = merlin_magic.agrvate_results, + agrvate_agr_group = merlin_magic.agrvate_agr_group, + agrvate_agr_match_score = merlin_magic.agrvate_agr_match_score, + agrvate_agr_canonical = merlin_magic.agrvate_agr_canonical, + agrvate_agr_multiple = merlin_magic.agrvate_agr_multiple, + agrvate_agr_num_frameshifts = merlin_magic.agrvate_agr_num_frameshifts, + agrvate_version = merlin_magic.agrvate_version, + agrvate_docker = merlin_magic.agrvate_docker, + emmtyper_emm_type = merlin_magic.emmtyper_emm_type, + emmtyper_results_tsv = merlin_magic.emmtyper_results_tsv, + emmtyper_version = merlin_magic.emmtyper_version, + emmtyper_docker = merlin_magic.emmtyper_docker, + pasty_serogroup = merlin_magic.pasty_serogroup, + pasty_serogroup_coverage = merlin_magic.pasty_serogroup_coverage, + pasty_serogroup_fragments = merlin_magic.pasty_serogroup_fragments, + pasty_summary_tsv = merlin_magic.pasty_summary_tsv, + pasty_blast_hits = merlin_magic.pasty_blast_hits, + pasty_all_serogroups = merlin_magic.pasty_all_serogroups, + pasty_version = merlin_magic.pasty_version, + pasty_docker = merlin_magic.pasty_docker, + pasty_comment = merlin_magic.pasty_comment, + qc_check = qc_check_task.qc_check, + qc_standard = qc_check_task.qc_standard, + hicap_serotype = merlin_magic.hicap_serotype, + hicap_genes = merlin_magic.hicap_genes, + hicap_results_tsv = merlin_magic.hicap_results_tsv, + hicap_version = merlin_magic.hicap_version, + hicap_docker = merlin_magic.hicap_docker, + abricate_vibrio_detailed_tsv = merlin_magic.abricate_vibrio_detailed_tsv, + abricate_vibrio_database = merlin_magic.abricate_vibrio_database, + abricate_vibrio_docker = merlin_magic.abricate_vibrio_docker, + abricate_vibrio_version = merlin_magic.abricate_vibrio_version, + abricate_vibrio_ctxA = merlin_magic.abricate_vibrio_ctxA, + abricate_vibrio_ompW = merlin_magic.abricate_vibrio_ompW, + abricate_vibrio_toxR = merlin_magic.abricate_vibrio_toxR, + abricate_vibrio_biotype = merlin_magic.abricate_vibrio_biotype, + abricate_vibrio_serogroup = merlin_magic.abricate_vibrio_serogroup + } } } } From 8d4581d63c132796f5c23f7475476729e2eeeeef Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 17 Jul 2024 18:54:42 +0000 Subject: [PATCH 2/4] move gambit into characterization boolean --- workflows/theiaprok/wf_theiaprok_fasta.wdl | 10 +++++----- workflows/theiaprok/wf_theiaprok_illumina_pe.wdl | 10 +++++----- workflows/theiaprok/wf_theiaprok_illumina_se.wdl | 10 +++++----- workflows/theiaprok/wf_theiaprok_ont.wdl | 11 +++++------ 4 files changed, 20 insertions(+), 21 deletions(-) diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index 9c5fb4498..70dca5eb6 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -56,17 +56,17 @@ workflow theiaprok_fasta { assembly = assembly_fasta, samplename = samplename } - call gambit_task.gambit { - input: - assembly = assembly_fasta, - samplename = samplename - } call busco_task.busco { input: assembly = assembly_fasta, samplename = samplename } if (perform_characterization) { + call gambit_task.gambit { + input: + assembly = assembly_fasta, + samplename = samplename + } if (call_ani) { call ani_task.animummer as ani { input: diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl index 79aa30564..fd2e7dea1 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl @@ -133,17 +133,17 @@ workflow theiaprok_illumina_pe { samplename = samplename, genome_length = select_first([genome_length, quast.genome_length]) } - call gambit_task.gambit { - input: - assembly = shovill_pe.assembly_fasta, - samplename = samplename - } call busco_task.busco { input: assembly = shovill_pe.assembly_fasta, samplename = samplename } if (perform_characterization) { + call gambit_task.gambit { + input: + assembly = shovill_pe.assembly_fasta, + samplename = samplename + } if (call_ani) { call ani_task.animummer as ani { input: diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index 1b6aa9f91..fdf577de8 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -126,17 +126,17 @@ workflow theiaprok_illumina_se { samplename = samplename, genome_length = select_first([genome_length, quast.genome_length]) } - call gambit_task.gambit { - input: - assembly = shovill_se.assembly_fasta, - samplename = samplename - } call busco_task.busco { input: assembly = shovill_se.assembly_fasta, samplename = samplename } if (perform_characterization) { + call gambit_task.gambit { + input: + assembly = shovill_se.assembly_fasta, + samplename = samplename + }\ if (call_ani) { call ani_task.animummer as ani { input: diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 742c21191..569ab5a60 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -121,18 +121,17 @@ workflow theiaprok_ont { samplename = samplename, est_genome_length = select_first([genome_length, quast.genome_length]) } - call gambit_task.gambit { - input: - assembly = dragonflye.assembly_fasta, - samplename = samplename - } call busco_task.busco { input: assembly = dragonflye.assembly_fasta, samplename = samplename } if (perform_characterization) { - + call gambit_task.gambit { + input: + assembly = dragonflye.assembly_fasta, + samplename = samplename + } if (call_ani) { call ani_task.animummer as ani { input: From db2d9bc060ba5b7dd9e419b194d4c57a8b64d349 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 17 Jul 2024 18:59:00 +0000 Subject: [PATCH 3/4] make gambit outputs optional and fix typo --- workflows/theiaprok/wf_theiaprok_fasta.wdl | 14 +++++++------- workflows/theiaprok/wf_theiaprok_illumina_se.wdl | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index 70dca5eb6..3735bda10 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -464,13 +464,13 @@ workflow theiaprok_fasta { String busco_results = busco.busco_results File? busco_report = busco.busco_report # Taxon ID - File gambit_report = gambit.gambit_report_file - File gambit_closest_genomes = gambit.gambit_closest_genomes_file - String gambit_predicted_taxon = gambit.gambit_predicted_taxon - String gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank - String gambit_version = gambit.gambit_version - String gambit_db_version = gambit.gambit_db_version - String gambit_docker = gambit.gambit_docker + File? gambit_report = gambit.gambit_report_file + File? gambit_closest_genomes = gambit.gambit_closest_genomes_file + String? gambit_predicted_taxon = gambit.gambit_predicted_taxon + String? gambit_predicted_taxon_rank = gambit.gambit_predicted_taxon_rank + String? gambit_version = gambit.gambit_version + String? gambit_db_version = gambit.gambit_db_version + String? gambit_docker = gambit.gambit_docker # ani-mummer Float? ani_highest_percent = ani.ani_highest_percent Float? ani_highest_percent_bases_aligned = ani.ani_highest_percent_bases_aligned diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index fdf577de8..0e00e3ac8 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -136,7 +136,7 @@ workflow theiaprok_illumina_se { input: assembly = shovill_se.assembly_fasta, samplename = samplename - }\ + } if (call_ani) { call ani_task.animummer as ani { input: From 3bc65777fa48c4dcbed4ede15e123ecfaf210793 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 17 Jul 2024 19:55:53 +0000 Subject: [PATCH 4/4] update md5sums --- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 32f1d9eb7..c966a3a77 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -633,7 +633,7 @@ - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl md5sum: 14565031f96d01ee6480bb0f9d19551d - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl - md5sum: 646e726beb68fc61f84a428bf2fb7244 + md5sum: 6d9dd969e2144ca23f2a0e101e6b6966 - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl md5sum: 43367523b9140ca0d2ac15869046343c - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index 4d821d96f..5c18a09bb 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -596,7 +596,7 @@ - path: miniwdl_run/wdl/tasks/utilities/data_export/task_broad_terra_tools.wdl md5sum: 14565031f96d01ee6480bb0f9d19551d - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl - md5sum: 347c054f9850e885e6a130d1655765d7 + md5sum: 5aa25e4fad466f92c96a7c138aca0d20 - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl md5sum: 43367523b9140ca0d2ac15869046343c - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl