Move hardcoded parameters to the config file

nextstrain · Mar 6, 2024 · f2c287a · f2c287a
1 parent a91e575
commit f2c287a
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Showing 4 changed files with 29 additions and 11 deletions.
diff --git a/phylogenetic/defaults/config_zika.yaml b/phylogenetic/defaults/config_zika.yaml
@@ -1,2 +1,20 @@
 strain_id_field: "accession"
-display_strain_field: "strain"
+display_strain_field: "strain"
+
+filter:
+  group_by: "country year month"
+  sequences_per_group: 40
+  min_date: 2012
+  min_length: 5385
+
+refine:
+  coalescent: "opt"
+  date_inference: "marginal"
+  clock_filter_iqd: 4
+
+ancestral:
+  inference: "joint"
+
+traits:
+  columns: "region country"
+  sampling_bias_correction: 3
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -39,7 +39,7 @@ rule ancestral:
     output:
         node_data = "results/nt_muts.json"
     params:
-        inference = "joint"
+        inference = config["ancestral"]["inference"]
     shell:
         """
         augur ancestral \
@@ -77,8 +77,8 @@ rule traits:
     output:
         node_data = "results/traits.json",
     params:
-        columns = "region country",
-        sampling_bias_correction = 3,
+        columns = config["traits"]["columns"],
+        sampling_bias_correction = config["traits"]["sampling_bias_correction"],
         strain_id = config.get("strain_id_field", "strain"),
     shell:
         """

diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk
@@ -48,9 +48,9 @@ rule refine:
         tree = "results/tree.nwk",
         node_data = "results/branch_lengths.json"
     params:
-        coalescent = "opt",
-        date_inference = "marginal",
-        clock_filter_iqd = 4,
+        coalescent = config["refine"]["coalescent"],
+        date_inference = config["refine"]["date_inference"],
+        clock_filter_iqd = config["refine"]["clock_filter_iqd"],
         strain_id = config.get("strain_id_field", "strain"),
     shell:
         """

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -64,10 +64,10 @@ rule filter:
     output:
         sequences = "results/filtered.fasta"
     params:
-        group_by = "country year month",
-        sequences_per_group = 40,
-        min_date = 2012,
-        min_length = 5385,
+        group_by = config["filter"]["group_by"],
+        sequences_per_group = config["filter"]["sequences_per_group"],
+        min_date = config["filter"]["min_date"],
+        min_length = config["filter"]["min_length"],
         strain_id = config.get("strain_id_field", "strain"),
     shell:
         """