diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index f4cda04e4..317dc5689 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -512,7 +512,7 @@ - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl md5sum: 64caaaff5910ac0036e2659434500962 - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl - md5sum: 3e31a3a359aafdff3e2c8f8411dc5c40 + md5sum: cea2e72701662adca0b30fd48baca3ab - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl md5sum: e797bbc7ceb4f62728f7ef315d9a4e40 - 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 03ae75323..b641a7fd7 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -483,7 +483,7 @@ - path: miniwdl_run/wdl/tasks/taxon_id/contamination/task_midas.wdl md5sum: 64caaaff5910ac0036e2659434500962 - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl - md5sum: 3d2fbc48cdb614b3f7ecbf576e1a3ee7 + md5sum: ff0f911bbaf3876ecb139bf6c564f1df - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl md5sum: e797bbc7ceb4f62728f7ef315d9a4e40 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index 1d0ae9d6a..46ffda542 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -218,7 +218,6 @@ workflow theiaprok_fasta { "amrfinderplus_version": amrfinderplus_task.amrfinderplus_version, "amrfinderplus_virulence_genes": amrfinderplus_task.amrfinderplus_virulence_genes, "amrfinderplus_virulence_report": amrfinderplus_task.amrfinderplus_virulence_report, - "ani_docker": ani.ani_docker, "ani_highest_percent": ani.ani_highest_percent, "ani_highest_percent_bases_aligned": ani.ani_highest_percent_bases_aligned, "ani_mummer_docker": ani.ani_docker, @@ -228,6 +227,7 @@ workflow theiaprok_fasta { "assembly_length": quast.genome_length, "bakta_gbff": bakta.bakta_gbff, "bakta_gff3": bakta.bakta_gff3, + "bakta_plot": bakta.bakta_plot, "bakta_summary": bakta.bakta_txt, "bakta_tsv": bakta.bakta_tsv, "bakta_version": bakta.bakta_version, @@ -253,13 +253,6 @@ workflow theiaprok_fasta { "gambit_predicted_taxon_rank": gambit.gambit_predicted_taxon_rank, "gambit_report": gambit.gambit_report_file, "gambit_version": gambit.gambit_version, - "genotyphi_final_genotype": merlin_magic.genotyphi_final_genotype, - "genotyphi_genotype_confidence": merlin_magic.genotyphi_genotype_confidence, - "genotyphi_mykrobe_json": merlin_magic.genotyphi_mykrobe_json, - "genotyphi_report_tsv": merlin_magic.genotyphi_report_tsv, - "genotyphi_species": merlin_magic.genotyphi_species, - "genotyphi_st_probes_percent_coverage": merlin_magic.genotyphi_st_probes_percent_coverage, - "genotyphi_version": merlin_magic.genotyphi_version, "hicap_docker": merlin_magic.hicap_docker, "hicap_genes": merlin_magic.hicap_genes, "hicap_results_tsv": merlin_magic.hicap_results_tsv, @@ -374,62 +367,25 @@ workflow theiaprok_fasta { "resfinder_seqs": resfinder_task.resfinder_hit_in_genome_seq, "run_id": run_id, "seq_platform": seq_method, - "seqsero2_predicted_antigenic_profile": merlin_magic.seqsero2_predicted_antigenic_profile, - "seqsero2_predicted_contamination": merlin_magic.seqsero2_predicted_contamination, - "seqsero2_predicted_serotype": merlin_magic.seqsero2_predicted_serotype, - "seqsero2_report": merlin_magic.seqsero2_report, - "seqsero2_version": merlin_magic.seqsero2_version, - "seroba_ariba_identity": merlin_magic.seroba_ariba_identity, - "seroba_ariba_serotype": merlin_magic.seroba_ariba_serotype, - "seroba_details": merlin_magic.seroba_details, - "seroba_docker": merlin_magic.seroba_docker, - "seroba_serotype": merlin_magic.seroba_serotype, - "seroba_version": merlin_magic.seroba_version, "serotypefinder_docker": merlin_magic.serotypefinder_docker, "serotypefinder_report": merlin_magic.serotypefinder_report, "serotypefinder_serotype": merlin_magic.serotypefinder_serotype, - "shigatyper_docker": merlin_magic.shigatyper_docker, - "shigatyper_hits_tsv": merlin_magic.shigatyper_hits_tsv, - "shigatyper_ipaB_presence_absence": merlin_magic.shigatyper_ipaB_presence_absence, - "shigatyper_notes": merlin_magic.shigatyper_notes, - "shigatyper_predicted_serotype": merlin_magic.shigatyper_predicted_serotype, - "shigatyper_summary_tsv": merlin_magic.shigatyper_summary_tsv, - "shigatyper_version": merlin_magic.shigatyper_version, "shigeifinder_H_antigen": merlin_magic.shigeifinder_H_antigen, - "shigeifinder_H_antigen_reads": merlin_magic.shigeifinder_H_antigen_reads, "shigeifinder_O_antigen": merlin_magic.shigeifinder_O_antigen, - "shigeifinder_O_antigen_reads": merlin_magic.shigeifinder_O_antigen_reads, "shigeifinder_cluster": merlin_magic.shigeifinder_cluster, - "shigeifinder_cluster_reads": merlin_magic.shigeifinder_cluster_reads, "shigeifinder_docker": merlin_magic.shigeifinder_docker, - "shigeifinder_docker_reads": merlin_magic.shigeifinder_docker_reads, "shigeifinder_ipaH_presence_absence": merlin_magic.shigeifinder_ipaH_presence_absence, - "shigeifinder_ipaH_presence_absence_reads": merlin_magic.shigeifinder_ipaH_presence_absence_reads, "shigeifinder_notes": merlin_magic.shigeifinder_notes, - "shigeifinder_notes_reads": merlin_magic.shigeifinder_notes_reads, "shigeifinder_num_virulence_plasmid_genes": merlin_magic.shigeifinder_num_virulence_plasmid_genes, - "shigeifinder_num_virulence_plasmid_genes_reads": merlin_magic.shigeifinder_num_virulence_plasmid_genes_reads, "shigeifinder_report": merlin_magic.shigeifinder_report, - "shigeifinder_report_reads": merlin_magic.shigeifinder_report_reads, "shigeifinder_serotype": merlin_magic.shigeifinder_serotype, - "shigeifinder_serotype_reads": merlin_magic.shigeifinder_serotype_reads, "shigeifinder_version": merlin_magic.shigeifinder_version, - "shigeifinder_version_reads": merlin_magic.shigeifinder_version_reads, "sistr_allele_fasta": merlin_magic.sistr_allele_fasta, "sistr_allele_json": merlin_magic.sistr_allele_json, "sistr_cgmlst": merlin_magic.sistr_cgmlst, "sistr_predicted_serotype": merlin_magic.sistr_predicted_serotype, "sistr_results": merlin_magic.sistr_results, "sistr_version": merlin_magic.sistr_version, - "sonneityping_final_genotype": merlin_magic.sonneityping_final_genotype, - "sonneityping_final_report_tsv": merlin_magic.sonneityping_final_report_tsv, - "sonneityping_genotype_confidence": merlin_magic.sonneityping_genotype_confidence, - "sonneityping_genotype_name": merlin_magic.sonneityping_genotype_name, - "sonneityping_mykrobe_docker": merlin_magic.sonneityping_mykrobe_docker, - "sonneityping_mykrobe_report_csv": merlin_magic.sonneityping_mykrobe_report_csv, - "sonneityping_mykrobe_report_json": merlin_magic.sonneityping_mykrobe_report_json, - "sonneityping_mykrobe_version": merlin_magic.sonneityping_mykrobe_version, - "sonneityping_species": merlin_magic.sonneityping_species, "spatyper_docker": merlin_magic.spatyper_docker, "spatyper_repeats": merlin_magic.spatyper_repeats, "spatyper_tsv": merlin_magic.spatyper_tsv, @@ -449,14 +405,6 @@ workflow theiaprok_fasta { "stxtyper_report": merlin_magic.stxtyper_report, "stxtyper_stx_frameshifts_or_internal_stop_hits": merlin_magic.stxtyper_stx_frameshifts_or_internal_stop_hits, "stxtyper_version": merlin_magic.stxtyper_version, - "tbprofiler_dr_type": merlin_magic.tbprofiler_dr_type, - "tbprofiler_main_lineage": merlin_magic.tbprofiler_main_lineage, - "tbprofiler_output_bai": merlin_magic.tbprofiler_output_bai, - "tbprofiler_output_bam": merlin_magic.tbprofiler_output_bam, - "tbprofiler_output_file": merlin_magic.tbprofiler_output_file, - "tbprofiler_resistance_genes": merlin_magic.tbprofiler_resistance_genes, - "tbprofiler_sub_lineage": merlin_magic.tbprofiler_sub_lineage, - "tbprofiler_version": merlin_magic.tbprofiler_version, "theiaprok_fasta_analysis_date": version_capture.date, "theiaprok_fasta_version": version_capture.phb_version, "ts_mlst_allelic_profile": ts_mlst.ts_mlst_allelic_profile, diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl index 0458e2ab0..5ef2fdfa5 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl @@ -350,6 +350,7 @@ workflow theiaprok_illumina_pe { "assembly_length": quast.genome_length, "bakta_gbff": bakta.bakta_gbff, "bakta_gff3": bakta.bakta_gff3, + "bakta_plot": bakta.bakta_plot, "bakta_summary": bakta.bakta_txt, "bakta_tsv": bakta.bakta_tsv, "bakta_version": bakta.bakta_version, diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index 50f6dfc74..47fe8b002 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -327,6 +327,7 @@ workflow theiaprok_illumina_se { "assembly_length": quast.genome_length, "bakta_gbff": bakta.bakta_gbff, "bakta_gff3": bakta.bakta_gff3, + "bakta_plot": bakta.bakta_plot, "bakta_summary": bakta.bakta_txt, "bakta_tsv": bakta.bakta_tsv, "bakta_version": bakta.bakta_version, diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 4dd800856..6f896f072 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -305,6 +305,7 @@ workflow theiaprok_ont { "assembly_length": quast.genome_length, "bakta_gbff": bakta.bakta_gbff, "bakta_gff3": bakta.bakta_gff3, + "bakta_plot": bakta.bakta_plot, "bakta_summary": bakta.bakta_txt, "bakta_tsv": bakta.bakta_tsv, "bakta_version": bakta.bakta_version,