Global tree and separating out the WA-specific configs

phylogenetic/build-configs/washington-state/config.yaml

@@ -0,0 +1,40 @@
+# This configuration file contains the custom configurations parameters
+# for the Washington State phylogenetic build with custom rules and metadata
+
+# Use 'NY99' as the reference since it should be basel to the USA sequences
+reference: "defaults/reference.gb"
+# Use 'IS88' as the root strain on the phylogenetic tree to place samples within the global context
+root: "AF481864"
+
+# Pull in metadata and sequences from the ingest directory after it has been annotated with washington-state specific metadata
+input_metadata: "../ingest/results/metadata.tsv"
+input_sequences: "../ingest/results/sequences.fasta"
+
+# This command excludes all strains by default and then forces the inclusion of
+# the strains selected by the subsampling logic defined above.
+subsampling:
+  state: --query "state == 'WA'" --min-length '9800' --subsample-max-sequences 5000
+  neighboring_state: --query "state in ['CA', 'ID', 'OR', 'NV']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
+  region: --query "state in ['AZ','NM', 'CO', 'UT', 'WY', 'MT']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
+  country: --query "country == 'USA' and state not in ['WA', 'CA', 'ID', 'OR', 'NV','AZ','NM', 'CO', 'UT', 'WY', 'MT'] and accession != 'NC_009942'" --group-by state year --subsample-max-sequences 300 --min-length '9800'
+  force_include: --exclude-all --include ../nextclade/defaults/include.txt
+
+refine:
+  treetime_params: --coalescent opt --clock-filter-iqd 4 --date-inference marginal --date-confidence
+
+traits:
+  metadata_columns: [
+    'country',
+    'division',
+    'location',
+    'clade_membership',
+    'host'
+  ]
+
+export:
+  auspice_config: "defaults/auspice_config.json"
+
+## Custom rules to run as part of the CI automated workflow
+## The paths should be relative to the phylogenetic directory.
+custom_rules:
+  - build-configs/washington-state/washington-state-rules.smk

phylogenetic/build-configs/washington-state/washington-state-rules.smk

@@ -0,0 +1,77 @@
+"""
+These are washington specific rules for the phylogenetic workflow.
+"""
+
+rule create_lat_longs:
+    """
+    This rule creates an averaged lat_longs.tsv file from the metadata_filtered.tsv file, but this requires a USA state annotation. This rule fails on global datasets.
+    """
+    input:
+        metadata = "results/metadata_filtered.tsv"
+    output:
+        lat_longs = "results/lat_longs.tsv"
+    log:
+        "logs/lat_longs.txt",
+    benchmark:
+        "benchmarks/lat_longs.txt"
+    shell:
+        """
+        python ./scripts/create_lat_longs.py {input.metadata} {output.lat_longs} 2>&1 | tee {log}
+        """
+
+
+rule create_colors:
+    input:
+        metadata = "results/metadata_filtered.tsv"
+    output:
+        colors = "results/colors.tsv"
+    log:
+            "logs/colors.txt",
+    benchmark:
+            "benchmarks/colors.txt"
+    shell:
+        """
+        python ./scripts/make_colors.py {input.metadata} {output.colors} 2>&1 | tee {log}
+        """
+
+
+rule export_washington_build:
+    """
+    This part of the workflow collects the phylogenetic tree and annotations to
+    export a Nextstrain dataset.
+    This includes incorporating the lat_long.tsv annotation.
+    """
+    input:
+        tree = "results/tree.nwk",
+        metadata = "results/metadata_filtered.tsv",
+        branch_lengths = "results/branch_lengths.json",
+        traits = "results/traits.json",
+        nt_muts = "results/nt_muts.json",
+        aa_muts = "results/aa_muts.json",
+        colors = "results/colors.tsv",
+        description = config["export"]["description"],
+        lat_longs = "results/lat_longs.tsv",
+        auspice_config = config["export"]["auspice_config"],
+    output:
+        auspice = "auspice/WNV_genome.json"
+    log:
+        "logs/export.txt",
+    benchmark:
+        "benchmarks/export.txt"
+    shell:
+        """
+        augur export v2 \
+            --tree {input.tree} \
+            --metadata {input.metadata} \
+            --metadata-id-columns "accession" \
+            --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
+            --colors {input.colors} \
+            --lat-longs {input.lat_longs} \
+            --description {input.description} \
+            --auspice-config {input.auspice_config} \
+            --output {output.auspice} 2>&1 | tee {log}
+        """
+
+# Add a Snakemake ruleorder directive here if you need to resolve ambiguous rules
+# that have the same output as the copy_example_data rule.
+ruleorder: export_washington_build > export

phylogenetic/defaults/auspice_config_global.json

@@ -0,0 +1,31 @@
+{
+  "title": "Global West Nile Virus Build",
+  "colorings": [
+    {"key": "gt", "title": "Genotype", "type": "categorical"},
+    {"key": "num_date", "title": "Sampling Date", "type": "continuous"},
+    {"key": "region", "title": "Region", "type": "categorical"},
+    {"key": "country", "title": "Country", "type": "categorical"},
+    {"key": "author", "title": "Authors", "type": "categorical"},
+    {"key": "host", "title": "Host Species", "type": "categorical"}
+  ],
+  "geo_resolutions": [
+    "region",
+    "country"
+  ],
+  "maintainers": [
+    {"name": "Marcela Torres", "url": "https://github.com/NW-PaGe/WNV-nextstrain"},
+    {"name": "NW-PaGe", "url": "https://github.com/NW-PaGe/WNV-nextstrain"},
+    {"name": "Nextstrain Team", "url": "https://next.nextstrain.org/"}
+  ],
+  "filters": [
+    "region",
+    "country",
+    "author",
+    "host"
+  ],
+  "display_defaults": {
+    "color_by": "region",
+    "map_triplicate": true,
+    "geo_resolution": "country"
+ }
+}

phylogenetic/defaults/config.yaml

@@ -1,9 +1,8 @@
 strain_id_field: "accession"
-# Use 'NY99' as the reference since it should be basel to the USA sequences
-reference: "defaults/reference.gb"
-# Use 'IS88' as the root strain on the phylogenetic tree
-# To place samples within the global context
-root: "AF481864"
+# Use 'Egypt 1951' as the reference and root, following Mencattelli et al, 2023
+# https://www.nature.com/articles/s41467-023-42185-7
+reference: "defaults/reference_global.gb"
+root: "AF260968"
 
 # Sequences must be FASTA and metadata must be TSV
 # Both files must be zstd compressed
@@ -66,22 +65,18 @@ input_sequences: "data/sequences.fasta"
 # This command excludes all strains by default and then forces the inclusion of
 # the strains selected by the subsampling logic defined above.
 subsampling:
-  state: --query "state == 'WA'" --min-length '9800' --subsample-max-sequences 5000
-  neighboring_state: --query "state in ['CA', 'ID', 'OR', 'NV']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
-  region: --query "state in ['AZ','NM', 'CO', 'UT', 'WY', 'MT']" --group-by state year --min-length '9800' --subsample-max-sequences 5000
-  country: --query "country == 'USA' and state not in ['WA', 'CA', 'ID', 'OR', 'NV','AZ','NM', 'CO', 'UT', 'WY', 'MT'] and accession != 'NC_009942'" --group-by state year --subsample-max-sequences 300 --min-length '9800'
-  force_include: --exclude-all --include ../nextclade/defaults/include.txt
-   #global: --query "country != 'USA'" --group-by country year --subsample-max-sequences 200
+  region: --query "is_lab_host != 'true'" --query-columns is_lab_host:str --min-length '9800' --group-by region year --subsample-max-sequences 3000 --exclude defaults/exclude.txt
+  force_include: --exclude-all --include defaults/include.txt
+
+refine:
+  treetime_params: --coalescent opt --date-inference marginal --date-confidence
 
 traits:
   metadata_columns: [
-    'country',
-    'division',
-    'location',
-    'clade_membership',
-    'host'
+    'region',
+    'country'
   ]
 
 export:
   description: "defaults/description.md"
-  auspice_config: "defaults/auspice_config.json"
+  auspice_config: "defaults/auspice_config_global.json"

phylogenetic/defaults/exclude.txt

@@ -0,0 +1,55 @@
+HW816192 # 11029 bp PAT 27-MAY-2015
+CS543188 # 11029 bp PAT 20-APR-2007
+CS568914 # 11029 bp PAT 18-MAY-2007
+CS568916 # 11029 bp PAT 18-MAY-2007
+CS568917 # 11029 bp PAT 18-MAY-2007
+CS568918 # 11029 bp PAT 18-MAY-2007
+CS568919 # 11029 bp PAT 18-MAY-2007
+FV537222 # 10962 bp PAT 18-MAR-2010
+FV537223 # 10962 bp PAT 18-MAR-2010
+FV537224 # 10962 bp PAT 18-MAR-2010
+FV537225 # 10962 bp PAT 18-MAR-2010
+LQ460608 #  8839 bp PAT 06-OCT-2016
+LQ564350 #  8839 bp PAT 06-OCT-2016
+LY683288 # 11062 bp PAT 04-DEC-2019
+MA388207 #  8839 bp PAT 30-OCT-2018
+HC467807 # 11029 bp PAT 21-APR-2010
+HH961658 # 10975 bp PAT 31-OCT-2010
+HH961659 # 11029 bp PAT 31-OCT-2010
+HV572312 # 11029 bp PAT 31-MAY-2012
+OP846974 # Suspected recombinant sequences from Mencattelli et al, 2023 https://www.nature.com/articles/s41467-023-42185-7
+OK239667 # Suspected recombinant sequences from Mencattelli et al, 2023 https://www.nature.com/articles/s41467-023-42185-7
+OM202920 # Clusters below PAT FV537222
+OM202936 # Clusters below PAT FV537222
+OM202914 # Clusters below PAT FV537222
+OM202933 # Clusters below PAT FV537222
+OM202907 # Clusters below PAT FV537222
+OK573263 # Clusters below PAT FV537222
+FV537224 # Clusters below PAT FV537222
+OK573278 # Clusters below PAT FV537222
+OM202917 # Clusters below PAT FV537222
+OM202919 # Clusters below PAT FV537222
+OM202910 # Clusters below PAT FV537222
+OM202911 # Clusters below PAT FV537222
+OM202922 # Clusters below PAT FV537222
+OK573272 # Clusters below PAT FV537222
+OK573262 # Clusters below PAT FV537222
+OK573279 # Clusters below PAT FV537222
+OK573269 # Clusters below PAT FV537222
+OM202923 # Clusters below PAT FV537222
+OM202906 # Clusters below PAT FV537222
+OM202909 # Clusters below PAT FV537222
+OM202930 # Clusters below PAT FV537222
+OM202929 # Clusters below PAT FV537222
+OM202904 # Clusters below PAT FV537222
+OM202913 # Clusters below PAT FV537222
+OM202908 # Clusters below PAT FV537222
+OM202915 # Clusters below PAT FV537222
+OM202912 # Clusters below PAT FV537222
+OK572999 # Clusters below PAT FV537222
+OK573277 # Clusters below PAT FV537222
+FV537225 # Clusters below PAT FV537222
+OM202905 # Clusters below PAT FV537222
+OM202932 # Clusters below PAT FV537222
+FV537223 # Clusters below PAT FV537222
+FV537222 # Clusters below PAT FV537222

phylogenetic/defaults/include.txt

@@ -0,0 +1,70 @@
+AF260968 # Egypt 1951
+NC_001563 # Lineage 2 reference
+NC_009942 # Lineage 1 reference
+HM051416 # Isreal 1953
+GQ851607 # Nigeria 1965
+GQ851606 # Senegal 1979
+AF481864 # pre-NY
+MH166901 # NY99
+MH166903 # NY99
+MH166904 # NY99
+KX547395 # NY99
+KX547519 # NY99
+KX547602 # NY99
+HM488130 # NY99
+HM488132 # NY99
+HQ671707 # NY99
+AF202541 # NY99
+AF206518 # NY99
+HM488127 # NY99
+HM488126 # NY99
+KX547410 # WN02
+KJ501434 # WN02
+KX547456 # WN02
+KY216155 # WN02
+KX547460 # WN02
+MF175829 # WN02
+KX547482 # WN02
+MF175827 # WN02
+MF175839 # WN02
+KT020853 # WN02
+KX547548 # WN02
+MF175863 # WN02
+KX547286 # WN02
+MF175873 # WN02
+MF175865 # WN02
+MF175831 # WN02
+MF175858 # WN02
+KJ501117 # SW03
+KJ501120 # SW03
+MF175815 # SW03
+MG004533 # SW03
+KF704147 # SW03
+KF704153 # SW03
+KR348940 # SW03
+KR348937 # SW03
+KX547361 # SW03
+JX015523 # SW03
+KR348944 # SW03
+KJ501124 # SW03
+KX547552 # SW03
+KJ145829 # SW03
+KR348981 # SW03
+KJ501118 # SW03
+KR348938 # SW03
+KR348976 # SW03
+KJ501170 # SW03
+KR348993 # SW03
+JQ700438 # SW03
+KR348977 # SW03
+KR348942 # SW03
+KR348941 # SW03
+KJ501121 # SW03
+KJ501122 # SW03
+KX547375 # SW03
+KM012172 # SW03
+KC333375 # SW03
+KJ501222 # SW03
+MG004537 # SW03
+MF175866 # SW03
+MG004540 # SW03