diff --git a/profiles/example/builds.yaml b/profiles/example/builds.yaml index 3d85d062..8c21f4ae 100644 --- a/profiles/example/builds.yaml +++ b/profiles/example/builds.yaml @@ -1,25 +1,9 @@ -# Define inputs. -data_source: fauna -fauna_fasta_fields: - - strain - - virus - - locus - - accession - - collection_date - - virus_inclusion_date - - region - - country - - division - - location - - passage_category - - originating_lab - - submitting_lab - - age - - gender +custom_rules: + - profiles/ci/prepare_data.smk + fasta_fields: - strain - virus - - segment - accession - date - date_submitted @@ -62,8 +46,7 @@ builds: tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt" clades: "config/h3n2/ha/clades.tsv" lineage: "h3n2" - min_date: "2019-01-01" auspice_config: "config/h3n2/auspice_config.json" subsamples: global: - filters: "--group-by region year month --subsample-max-sequences 200 --min-date 2019-01-01 --exclude-where 'ha!=True' 'na!=True'" + filters: "--exclude-where 'ha!=True' 'na!=True'"