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add Flu NA Nextclade outputs to theiacov_illumina_pe #406

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merged 2 commits into from
Apr 11, 2024
Merged

add Flu NA Nextclade outputs to theiacov_illumina_pe #406

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5301eb8
add Flu NA Nextclade outputs to theiacov_illumina_pe. need to test in…
kapsakcj Apr 10, 2024
8a7af9c
added Flu NA nextclade outputs to theiacov_ont workflow. need to test…
kapsakcj Apr 10, 2024
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5 changes: 5 additions & 0 deletions workflows/theiacov/wf_theiacov_illumina_pe.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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5 changes: 5 additions & 0 deletions workflows/theiacov/wf_theiacov_ont.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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