From a2c727c214529db05a9fc6267e87b244899bcf24 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Wed, 20 Sep 2023 10:06:23 -0400 Subject: [PATCH] added 2 new resfinder string outputs to TheiaProk workflows (FASTA, SE, ONT). also added to export_taxon_tables inputs. renamed call block alias for resfinder in theiaprok_ONT to match other workflows --- workflows/theiaprok/wf_theiaprok_fasta.wdl | 4 ++ .../theiaprok/wf_theiaprok_illumina_se.wdl | 4 ++ workflows/theiaprok/wf_theiaprok_ont.wdl | 38 ++++++++++--------- 3 files changed, 29 insertions(+), 17 deletions(-) diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl index cf4f7df7b..ca9990115 100644 --- a/workflows/theiaprok/wf_theiaprok_fasta.wdl +++ b/workflows/theiaprok/wf_theiaprok_fasta.wdl @@ -184,6 +184,8 @@ workflow theiaprok_fasta { 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_db_version = resfinder_task.resfinder_db_version, resfinder_docker = resfinder_task.resfinder_docker, ts_mlst_results = ts_mlst.ts_mlst_results, @@ -431,6 +433,8 @@ workflow theiaprok_fasta { File? resfinder_results = resfinder_task.resfinder_results_tab File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table File? resfinder_pointfinder_results = resfinder_task.pointfinder_results + String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance + String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella String? resfinder_db_version = resfinder_task.resfinder_db_version String? resfinder_docker = resfinder_task.resfinder_docker # MLST Typing diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl index 4f2025bd6..d1d016187 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl @@ -282,6 +282,8 @@ workflow theiaprok_illumina_se { 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_db_version = resfinder_task.resfinder_db_version, resfinder_docker = resfinder_task.resfinder_docker, ts_mlst_results = ts_mlst.ts_mlst_results, @@ -577,6 +579,8 @@ workflow theiaprok_illumina_se { File? resfinder_results = resfinder_task.resfinder_results_tab File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table File? resfinder_pointfinder_results = resfinder_task.pointfinder_results + String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance + String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella String? resfinder_db_version = resfinder_task.resfinder_db_version String? resfinder_docker = resfinder_task.resfinder_docker # MLST Typing diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl index 6057ddce0..4a0732c61 100644 --- a/workflows/theiaprok/wf_theiaprok_ont.wdl +++ b/workflows/theiaprok/wf_theiaprok_ont.wdl @@ -138,7 +138,7 @@ workflow theiaprok_ont { organism = select_first([expected_taxon, gambit.gambit_predicted_taxon]) } if (call_resfinder) { - call resfinder_task.resfinder { + call resfinder_task.resfinder as resfinder_task { input: assembly = dragonflye.assembly_fasta, samplename = samplename, @@ -274,14 +274,16 @@ workflow theiaprok_ont { amrfinderplus_amr_subclasses = amrfinderplus.amrfinderplus_amr_subclasses, amrfinderplus_version = amrfinderplus.amrfinderplus_version, amrfinderplus_db_version = amrfinderplus.amrfinderplus_db_version, - resfinder_pheno_table = resfinder.resfinder_pheno_table, - resfinder_pheno_table_species = resfinder.resfinder_pheno_table_species, - resfinder_seqs = resfinder.resfinder_hit_in_genome_seq, - resfinder_results = resfinder.resfinder_results_tab, - resfinder_pointfinder_pheno_table = resfinder.pointfinder_pheno_table, - resfinder_pointfinder_results = resfinder.pointfinder_results, - resfinder_db_version = resfinder.resfinder_db_version, - resfinder_docker = resfinder.resfinder_docker, + 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_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, @@ -545,14 +547,16 @@ workflow theiaprok_ont { String? amrfinderplus_version = amrfinderplus.amrfinderplus_version String? amrfinderplus_db_version = amrfinderplus.amrfinderplus_db_version # Resfinder Outputs - File? resfinder_pheno_table = resfinder.resfinder_pheno_table - File? resfinder_pheno_table_species = resfinder.resfinder_pheno_table_species - File? resfinder_seqs = resfinder.resfinder_hit_in_genome_seq - File? resfinder_results = resfinder.resfinder_results_tab - File? resfinder_pointfinder_pheno_table = resfinder.pointfinder_pheno_table - File? resfinder_pointfinder_results = resfinder.pointfinder_results - String? resfinder_db_version = resfinder.resfinder_db_version - String? resfinder_docker = resfinder.resfinder_docker + File? resfinder_pheno_table = resfinder_task.resfinder_pheno_table + File? resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species + File? resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq + File? resfinder_results = resfinder_task.resfinder_results_tab + File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table + File? resfinder_pointfinder_results = resfinder_task.pointfinder_results + String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance + String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella + 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