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[Taxon_Table] resync taxon_tables inputs #762

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merged 2 commits into from
Feb 20, 2025
Merged

[Taxon_Table] resync taxon_tables inputs #762

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fbfb846
resync taxon_tables inputs
Feb 19, 2025
adbfd3d
update md5s
Feb 19, 2025
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2 changes: 1 addition & 1 deletion tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Expand Up @@ -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
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54 changes: 1 addition & 53 deletions workflows/theiaprok/wf_theiaprok_fasta.wdl
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Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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,
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1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
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Expand Up @@ -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,
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_illumina_se.wdl
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Expand Up @@ -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,
Expand Down
1 change: 1 addition & 0 deletions workflows/theiaprok/wf_theiaprok_ont.wdl
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Expand Up @@ -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,
Expand Down
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