Created
March 7, 2024 18:23
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Example subsampling logic for multi-species seasonal flu build
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| custom_rules: | |
| - profiles/gisaid/prepare_data.smk | |
| metadata_fields: | |
| - Isolate_Name | |
| - Isolate_Id | |
| - Passage_History | |
| - Location | |
| - Authors | |
| - Originating_Lab | |
| - Collection_Date | |
| - Submission_Date | |
| renamed_metadata_fields: | |
| - strain | |
| - accession | |
| - passage | |
| - location | |
| - authors | |
| - originating_lab | |
| - date | |
| - date_submitted | |
| lat-longs: "config/lat_longs.tsv" | |
| segments: | |
| - ha | |
| submission_date_field: date_submitted | |
| recency: | |
| date_bins: [7, 30, 90] | |
| date_bin_labels: ["last week", "last month", "last quarter"] | |
| upper_bin_label: older | |
| builds: | |
| "h3n2": | |
| lineage: h3n2 | |
| reference: "config/h3n2/{segment}/reference.fasta" | |
| annotation: "config/h3n2/{segment}/genemap.gff" | |
| tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt" | |
| clades: "config/h3n2/ha/clades.tsv" | |
| subclades: "config/h3n2/ha/subclades.tsv" | |
| auspice_config: "config/h3n2/auspice_config.json" | |
| enable_lbi: true | |
| enable_glycosylation: true | |
| subsamples: | |
| human: | |
| filters: --query "host == 'human'" --subsample-max-sequences 100 --group-by country year month | |
| avian: | |
| filters: --query "host in ['duck', 'chicken', 'stork']" --subsample-max-sequences 100 --group-by region | |
| swine: | |
| filters: --query "host == 'swine'" --subsample-max-sequences 100 --group-by region |
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| custom_rules: | |
| - profiles/gisaid/prepare_data.smk | |
| metadata_fields: | |
| - Isolate_Name | |
| - Isolate_Id | |
| - Passage_History | |
| - Location | |
| - Authors | |
| - Originating_Lab | |
| - Collection_Date | |
| - Submission_Date | |
| renamed_metadata_fields: | |
| - strain | |
| - accession | |
| - passage | |
| - location | |
| - authors | |
| - originating_lab | |
| - date | |
| - date_submitted | |
| lat-longs: "config/lat_longs.tsv" | |
| segments: | |
| - ha | |
| submission_date_field: date_submitted | |
| recency: | |
| date_bins: [7, 30, 90] | |
| date_bin_labels: ["last week", "last month", "last quarter"] | |
| upper_bin_label: older | |
| builds: | |
| "h3n2": | |
| lineage: h3n2 | |
| reference: "config/h3n2/{segment}/reference.fasta" | |
| annotation: "config/h3n2/{segment}/genemap.gff" | |
| tree_exclude_sites: "config/h3n2/{segment}/exclude-sites.txt" | |
| clades: "config/h3n2/ha/clades.tsv" | |
| subclades: "config/h3n2/ha/subclades.tsv" | |
| auspice_config: "config/h3n2/auspice_config.json" | |
| enable_lbi: true | |
| enable_glycosylation: true | |
| subsamples: | |
| specific_strains: | |
| filters: --exclude-all --include profiles/gisaid/specific_strains.txt |
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