From 5301eb8d6eb37f24bdc6be5969b394e1ba3b4820 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Wed, 10 Apr 2024 12:08:12 -0400 Subject: [PATCH 1/2] add Flu NA Nextclade outputs to theiacov_illumina_pe. need to test in Terra --- workflows/theiacov/wf_theiacov_illumina_pe.wdl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/workflows/theiacov/wf_theiacov_illumina_pe.wdl b/workflows/theiacov/wf_theiacov_illumina_pe.wdl index 22740c449..7d7deda1e 100644 --- a/workflows/theiacov/wf_theiacov_illumina_pe.wdl +++ b/workflows/theiacov/wf_theiacov_illumina_pe.wdl @@ -443,16 +443,21 @@ workflow theiacov_illumina_pe { String? pangolin_versions = pangolin4.pangolin_versions # Nextclade outputs String nextclade_json = select_first([nextclade_v3.nextclade_json, ""]) + String nextclade_json_flu_na = select_first([nextclade_flu_na.nextclade_json, ""]) String auspice_json = select_first([ nextclade_v3.auspice_json, ""]) + String auspice_json_flu_na = select_first([nextclade_flu_na.auspice_json, ""]) String nextclade_tsv = select_first([nextclade_v3.nextclade_tsv, ""]) + String nextclade_tsv_flu_na = select_first([nextclade_flu_na.nextclade_tsv, ""]) String nextclade_version = select_first([nextclade_v3.nextclade_version, ""]) String nextclade_docker = select_first([nextclade_v3.nextclade_docker, ""]) String nextclade_ds_tag = select_first([ha_na_nextclade_ds_tag, set_flu_ha_nextclade_values.nextclade_dataset_tag, organism_parameters.nextclade_dataset_tag, ""]) String nextclade_aa_subs = select_first([ha_na_nextclade_aa_subs, nextclade_output_parser.nextclade_aa_subs, ""]) String nextclade_aa_dels = select_first([ha_na_nextclade_aa_dels, nextclade_output_parser.nextclade_aa_dels, ""]) String nextclade_clade = select_first([nextclade_output_parser.nextclade_clade, ""]) + String nextclade_clade_flu_na = select_first([nextclade_output_parser_flu_na.nextclade_clade, ""]) String? nextclade_lineage = nextclade_output_parser.nextclade_lineage String? nextclade_qc = nextclade_output_parser.nextclade_qc + String? nextclade_qc_flu_na = nextclade_output_parser_flu_na.nextclade_qc # VADR Annotation QC File? vadr_alerts_list = vadr.alerts_list String? vadr_num_alerts = vadr.num_alerts From 8a7af9c9f1224f85bf58e27aa8873ce1ad39adc8 Mon Sep 17 00:00:00 2001 From: kapsakcj Date: Wed, 10 Apr 2024 12:18:45 -0400 Subject: [PATCH 2/2] added Flu NA nextclade outputs to theiacov_ont workflow. need to test in Terra --- workflows/theiacov/wf_theiacov_ont.wdl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/workflows/theiacov/wf_theiacov_ont.wdl b/workflows/theiacov/wf_theiacov_ont.wdl index 9b3e71a66..e12067e13 100644 --- a/workflows/theiacov/wf_theiacov_ont.wdl +++ b/workflows/theiacov/wf_theiacov_ont.wdl @@ -404,16 +404,21 @@ workflow theiacov_ont { String? pangolin_versions = pangolin4.pangolin_versions # Nextclade outputs String nextclade_json = select_first([nextclade_v3.nextclade_json, ""]) + String nextclade_json_flu_na = select_first([nextclade_flu_na.nextclade_json, ""]) String auspice_json = select_first([ nextclade_v3.auspice_json, ""]) + String auspice_json_flu_na = select_first([nextclade_flu_na.auspice_json, ""]) String nextclade_tsv = select_first([nextclade_v3.nextclade_tsv, ""]) + String nextclade_tsv_flu_na = select_first([nextclade_flu_na.nextclade_tsv, ""]) String nextclade_version = select_first([nextclade_v3.nextclade_version, ""]) String nextclade_docker = select_first([nextclade_v3.nextclade_docker, ""]) String nextclade_ds_tag = select_first([ha_na_nextclade_ds_tag, set_flu_ha_nextclade_values.nextclade_dataset_tag, organism_parameters.nextclade_dataset_tag, ""]) String nextclade_aa_subs = select_first([ha_na_nextclade_aa_subs, nextclade_output_parser.nextclade_aa_subs, ""]) String nextclade_aa_dels = select_first([ha_na_nextclade_aa_dels, nextclade_output_parser.nextclade_aa_dels, ""]) String nextclade_clade = select_first([nextclade_output_parser.nextclade_clade, ""]) + String nextclade_clade_flu_na = select_first([nextclade_output_parser_flu_na.nextclade_clade, ""]) String? nextclade_lineage = nextclade_output_parser.nextclade_lineage String? nextclade_qc = nextclade_output_parser.nextclade_qc + String? nextclade_qc_flu_na = nextclade_output_parser_flu_na.nextclade_qc # VADR Annotation QC File? vadr_alerts_list = vadr.alerts_list String? vadr_num_alerts = vadr.num_alerts