Move paths to clade definition files to configfile

nextstrain · Jan 8, 2024 · a3232c1 · a3232c1
1 parent 1a87f89
commit a3232c1
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Showing 3 changed files with 9 additions and 11 deletions.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -7,16 +7,6 @@ rule all:
     input:
         auspice_json = expand("auspice/dengue_{serotype}.json", serotype=serotypes)
 
-def clade_defs(w):
-    defs = {
-        'all': 'config/clades_serotypes.tsv',
-        'denv1': 'config/clades_genotypes.tsv',
-        'denv2': 'config/clades_genotypes.tsv',
-        'denv3': 'config/clades_genotypes.tsv',
-        'denv4': 'config/clades_genotypes.tsv'
-    }
-    return defs[w.serotype]
-
 include: "rules/prepare_sequences.smk"
 include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"

diff --git a/phylogenetic/config/config_dengue.yaml b/phylogenetic/config/config_dengue.yaml
@@ -20,3 +20,11 @@ traits:
     denv2: 'country region'
     denv3: 'country region'
     denv4: 'country region'
+
+clades:
+  clade_definitions:
+    all: 'config/clades_serotypes.tsv'
+    denv1: 'config/clades_genotypes.tsv'
+    denv2: 'config/clades_genotypes.tsv'
+    denv3: 'config/clades_genotypes.tsv'
+    denv4: 'config/clades_genotypes.tsv'
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -88,7 +88,7 @@ rule clades:
         tree = "results/tree_{serotype}.nwk",
         nt_muts = "results/nt-muts_{serotype}.json",
         aa_muts = "results/aa-muts_{serotype}.json",
-        clade_defs = clade_defs,
+        clade_defs = lambda wildcards: config['clades']['clade_definitions'][wildcards.serotype],
     output:
         clades = "results/clades_{serotype}.json"
     shell: