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| # | ||
| # TKTK | ||
| # | ||
| custom_rules: | ||
| - "rules/cattle-flu.smk" | ||
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| #### Parameters which define which builds to produce via this config ### | ||
| builds: | ||
| h5n1-d1.1: '' | ||
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| segments: | ||
| - genome | ||
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| #### Parameters which define the input source #### | ||
| s3_src: | ||
| name: gisaid | ||
| metadata: s3://nextstrain-data-private/files/workflows/avian-flu/metadata.tsv.zst | ||
| sequences: s3://nextstrain-data-private/files/workflows/avian-flu/{segment}/sequences.fasta.zst | ||
| local_ingest: false | ||
| # P.S. To use local ingest files, comment out s3_src and change to local_ingest: joined-ncbi (e.g.) | ||
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| #### Parameters which control large overarching aspects of the build | ||
| # Set a high target_sequences_per_tree to capture all circulating strains, as they will be pruned down | ||
| # as part of the workflow | ||
| target_sequences_per_tree: 10_000 | ||
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| #### Config files #### | ||
| reference: config/h5n1/reference_h5n1_{segment}.gb # use H5N1 references | ||
| genome_reference: config/h5n1-cattle-outbreak/h5_cattle_genome_root.gb # use cattle-flu genome reference TODO XXX | ||
| auspice_config: config/{subtype}/auspice_config_{subtype}.json | ||
| colors: config/h5n1/colors_h5n1.tsv # use H5N1 colors | ||
| lat_longs: config/h5n1/lat_longs_h5n1.tsv # use H5N1 lat-longs | ||
| include_strains: config/{subtype}/include_strains_{subtype}.txt | ||
| # use cattle-outbreak specific dropped strains for segment + genome trees | ||
| dropped_strains: config/{subtype}/dropped_strains_{subtype}.txt | ||
| clades_file: clade-labeling/h5n1-clades.tsv # use H5N1 clades | ||
| description: config/{subtype}/description.md | ||
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| #### Rule-specific parameters #### | ||
| filter: | ||
| min_length: | ||
| FALLBACK: | ||
| pb2: 2100 | ||
| pb1: 2100 | ||
| pa: 2000 | ||
| ha: 1600 | ||
| np: 1400 | ||
| na: 1270 | ||
| mp: 900 | ||
| ns: 800 | ||
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| min_date: | ||
| FALLBACK: 2024 | ||
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| group_by: | ||
| FALLBACK: false # no grouping during filter | ||
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| exclude_where: | ||
| FALLBACK: host=laboratoryderived host=ferret host=unknown host=other host=host gisaid_clade=3C.2 | ||
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| refine: | ||
| coalescent: const | ||
| date_inference: marginal | ||
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| genome_clock_filter_iqd: | ||
| FALLBACK: 6 | ||
| clock_filter_iqd: | ||
| FALLBACK: false | ||
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| root: | ||
| FALLBACK: false | ||
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| # For the genome only we use the closest outgroup as the root | ||
| # P.S. Make sure this strain is force included via augur filter --include | ||
| # (This isn't needed for the segment builds as we include a large enough time span to root via the clock) | ||
| genome_root: | ||
| FALLBACK: best | ||
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| segment_lengths: | ||
| FALLBACK: | ||
| {'pb2': 2341, 'pb1': 2341, 'pa': 2233, 'ha': 1760, 'np': 1565, 'na': 1458, 'mp': 1027, 'ns': 865} | ||
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| __clock_std_dev: &clock_std_dev 0.00211 # YAML anchor so we can reference this value below | ||
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| clock_rates: | ||
| FALLBACK: | ||
| # The rates for the 8 segments are taken from the GISAID H5N1/2y config | ||
| pb2: [0.00287, *clock_std_dev] | ||
| pb1: [0.00264, *clock_std_dev] | ||
| pa: [0.00248, *clock_std_dev] | ||
| ha: [0.00455, *clock_std_dev] | ||
| np: [0.00252, *clock_std_dev] | ||
| na: [0.00349, *clock_std_dev] | ||
| mp: [0.00191, *clock_std_dev] | ||
| ns: [0.00249, *clock_std_dev] | ||
| # the genome clock rate is calculated by a function in the snakemake pipeline | ||
| # using the segment rates weighted by their lengths | ||
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| ancestral: | ||
| inference: joint | ||
| root_seq: | ||
| FALLBACK: false | ||
| genome_root_seq: | ||
| FALLBACK: config/h5n1-cattle-outbreak/h5_cattle_genome_root.gb | ||
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| traits: | ||
| # genome build has different parameters... | ||
| genome_columns: | ||
| FALLBACK: division | ||
| genome_sampling_bias_correction: | ||
| FALLBACK: 5 | ||
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| # segment builds: | ||
| columns: | ||
| FALLBACK: region country # same as GISAID H5N1 builds | ||
| sampling_bias_correction: | ||
| FALLBACK: false | ||
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| # all builds | ||
| confidence: | ||
| FALLBACK: true | ||
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| export: | ||
| genome_title: | ||
| FALLBACK: false | ||
| title: | ||
| FALLBACK: false |
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| { | ||
| "title": "Full genome analysis of the ongoing influenza A/H5N1 D1.1 outbreak in North America", | ||
| "maintainers": [ | ||
| {"name": "Moncla lab", "url": "https://lmoncla.github.io/monclalab/"}, | ||
| {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"} | ||
| ], | ||
| "build_url": "https://github.com/nextstrain/avian-flu", | ||
| "data_provenance": [ | ||
| { | ||
| "name": "USDA", | ||
| "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1102327" | ||
| }, | ||
| { | ||
| "name": "GISAID" | ||
| } | ||
| ], | ||
| "extensions": { | ||
| "nextclade": { | ||
| "pathogen": { | ||
| "schemaVersion":"3.0.0", | ||
| "defaultCds": "HA", | ||
| "cdsOrderPreference":[ | ||
| "PB2", | ||
| "PB1", | ||
| "PA", | ||
| "HA", | ||
| "NP", | ||
| "NA", | ||
| "M1", | ||
| "M2", | ||
| "NS1", | ||
| "NS2" | ||
| ], | ||
| "attributes": { | ||
| "name": "H5N1 dairy cattle outbreak", | ||
| "reference name": "concatenated ancestral sequences", | ||
| "reference accession": "none" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "colorings": [ | ||
| { | ||
| "key": "gt", | ||
| "title": "Genotype", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "num_date", | ||
| "title": "Date", | ||
| "type": "continuous" | ||
| }, | ||
| { | ||
| "key": "region", | ||
| "title": "Region", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "country", | ||
| "title": "Country", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "division", | ||
| "title": "Admin Division", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "host", | ||
| "title": "Host", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "subtype", | ||
| "title": "Subtype", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "h5_label_clade", | ||
| "title": "Provisional LABEL Clade", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "furin_cleavage_motif", | ||
| "title": "Furin Cleavage Motif", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "cleavage_site_sequence", | ||
| "title": "Cleavage Site Sequence", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "author", | ||
| "title": "Authors", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "originating_lab", | ||
| "title": "Originating Lab", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "submitting_lab", | ||
| "title": "Submitting Lab", | ||
| "type": "categorical" | ||
| }, | ||
| { | ||
| "key": "data_source", | ||
| "title": "Data Source", | ||
| "type": "categorical" | ||
| } | ||
| ], | ||
| "geo_resolutions": [ | ||
| "region", | ||
| "country", | ||
| "division" | ||
| ], | ||
| "display_defaults": { | ||
| "map_triplicate": false, | ||
| "color_by": "host", | ||
| "geo_resolution": "division", | ||
| "distance_measure": "num_date" | ||
| }, | ||
| "filters": [ | ||
| "host", | ||
| "region", | ||
| "country", | ||
| "division", | ||
| "subtype", | ||
| "author", | ||
| "originating_lab", | ||
| "submitting_lab", | ||
| "data_source" | ||
| ], | ||
| "metadata_columns": [ | ||
| "genbank_accession", | ||
| "sra_accessions" | ||
| ] | ||
| } |
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