Rename phylogenetic/config to phylogenetic/defaults

To be more consistent with the pathogen-repo-guide and the ingest workflow
nextstrain · Dec 18, 2024 · cca844c · cca844c
1 parent 1a168b5
commit cca844c
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Showing 22 changed files with 19 additions and 19 deletions.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -1,4 +1,4 @@
-configfile: "config/config_dengue.yaml"
+configfile: "defaults/config_dengue.yaml"
 
 serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
 genes = ['genome', 'E']

diff --git a/phylogenetic/config/clades_genotypes.tsv → phylogenetic/defaults/clades_genotypes.tsv b/phylogenetic/config/clades_genotypes.tsv → phylogenetic/defaults/clades_genotypes.tsv
diff --git a/phylogenetic/config/clades_serotypes.tsv → phylogenetic/defaults/clades_serotypes.tsv b/phylogenetic/config/clades_serotypes.tsv → phylogenetic/defaults/clades_serotypes.tsv
diff --git a/phylogenetic/config/color_orderings.tsv → phylogenetic/defaults/color_orderings.tsv b/phylogenetic/config/color_orderings.tsv → phylogenetic/defaults/color_orderings.tsv
diff --git a/phylogenetic/config/color_schemes.tsv → phylogenetic/defaults/color_schemes.tsv b/phylogenetic/config/color_schemes.tsv → phylogenetic/defaults/color_schemes.tsv
diff --git a/phylogenetic/config/config_dengue.yaml → phylogenetic/defaults/config_dengue.yaml b/phylogenetic/config/config_dengue.yaml → phylogenetic/defaults/config_dengue.yaml
@@ -8,8 +8,8 @@ strain_id_field: "genbank_accession"
 display_strain_field: "strain"
 
 filter:
-  exclude: "config/exclude.txt"
-  include: "config/include_{serotype}.txt"
+  exclude: "defaults/exclude.txt"
+  include: "defaults/include_{serotype}.txt"
   group_by: "year region"
   min_length:
     genome: 5000
@@ -32,11 +32,11 @@ traits:
 
 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'
+    all: 'defaults/clades_serotypes.tsv'
+    denv1: 'defaults/clades_genotypes.tsv'
+    denv2: 'defaults/clades_genotypes.tsv'
+    denv3: 'defaults/clades_genotypes.tsv'
+    denv4: 'defaults/clades_genotypes.tsv'
 
 export:
-  description: "config/description.md"
+  description: "defaults/description.md"
diff --git a/phylogenetic/config/description.md → phylogenetic/defaults/description.md b/phylogenetic/config/description.md → phylogenetic/defaults/description.md
diff --git a/phylogenetic/config/exclude.txt → phylogenetic/defaults/exclude.txt b/phylogenetic/config/exclude.txt → phylogenetic/defaults/exclude.txt
diff --git a/phylogenetic/config/include_all.txt → phylogenetic/defaults/include_all.txt b/phylogenetic/config/include_all.txt → phylogenetic/defaults/include_all.txt
diff --git a/phylogenetic/config/include_denv1.txt → phylogenetic/defaults/include_denv1.txt b/phylogenetic/config/include_denv1.txt → phylogenetic/defaults/include_denv1.txt
diff --git a/phylogenetic/config/include_denv2.txt → phylogenetic/defaults/include_denv2.txt b/phylogenetic/config/include_denv2.txt → phylogenetic/defaults/include_denv2.txt
diff --git a/phylogenetic/config/include_denv3.txt → phylogenetic/defaults/include_denv3.txt b/phylogenetic/config/include_denv3.txt → phylogenetic/defaults/include_denv3.txt
diff --git a/phylogenetic/config/include_denv4.txt → phylogenetic/defaults/include_denv4.txt b/phylogenetic/config/include_denv4.txt → phylogenetic/defaults/include_denv4.txt
diff --git a/phylogenetic/config/reference_all_genome.gb → ...ogenetic/defaults/reference_all_genome.gb b/phylogenetic/config/reference_all_genome.gb → ...ogenetic/defaults/reference_all_genome.gb
diff --git a/...ogenetic/config/reference_denv1_genome.gb → ...enetic/defaults/reference_denv1_genome.gb b/...ogenetic/config/reference_denv1_genome.gb → ...enetic/defaults/reference_denv1_genome.gb
diff --git a/...ogenetic/config/reference_denv2_genome.gb → ...enetic/defaults/reference_denv2_genome.gb b/...ogenetic/config/reference_denv2_genome.gb → ...enetic/defaults/reference_denv2_genome.gb
diff --git a/...ogenetic/config/reference_denv3_genome.gb → ...enetic/defaults/reference_denv3_genome.gb b/...ogenetic/config/reference_denv3_genome.gb → ...enetic/defaults/reference_denv3_genome.gb
diff --git a/...ogenetic/config/reference_denv4_genome.gb → ...enetic/defaults/reference_denv4_genome.gb b/...ogenetic/config/reference_denv4_genome.gb → ...enetic/defaults/reference_denv4_genome.gb
diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk
@@ -44,7 +44,7 @@ rule translate:
     input:
         tree = "results/{gene}/tree_{serotype}.nwk",
         node_data = "results/{gene}/nt-muts_{serotype}.json",
-        reference = lambda wildcard: "config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb"
+        reference = lambda wildcard: "defaults/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/defaults/reference_{serotype}_{gene}.gb"
     output:
         node_data = "results/{gene}/aa-muts_{serotype}.json"
     shell:

diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk
@@ -22,8 +22,8 @@ import json
 
 rule colors:
     input:
-        color_schemes = "config/color_schemes.tsv",
-        color_orderings = "config/color_orderings.tsv",
+        color_schemes = "defaults/color_schemes.tsv",
+        color_orderings = "defaults/color_orderings.tsv",
         metadata = "data/metadata_{serotype}.tsv",
     output:
         colors = "results/colors_{serotype}.tsv"
@@ -40,7 +40,7 @@ rule colors:
 rule prepare_auspice_config:
     """Prepare the auspice config file for each serotypes"""
     output:
-        auspice_config="results/config/{gene}/auspice_config_{serotype}.json",
+        auspice_config="results/defaults/{gene}/auspice_config_{serotype}.json",
     params:
         replace_clade_key=lambda wildcard: r"clade_membership" if wildcard.gene in ['genome'] else r"genotype_nextclade",
         replace_clade_title=lambda wildcard: r"Serotype" if wildcard.serotype in ['all'] else r"Dengue Genotype (Nextclade)",
@@ -140,7 +140,7 @@ rule export:
         nt_muts = "results/{gene}/nt-muts_{serotype}.json",
         aa_muts = "results/{gene}/aa-muts_{serotype}.json",
         description = config["export"]["description"],
-        auspice_config = "results/config/{gene}/auspice_config_{serotype}.json",
+        auspice_config = "results/defaults/{gene}/auspice_config_{serotype}.json",
         colors = "results/colors_{serotype}.tsv",
     output:
         auspice_json = "results/{gene}/raw_dengue_{serotype}.json"

diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -85,7 +85,7 @@ rule align:
     """
     input:
         sequences = "results/{gene}/filtered_{serotype}.fasta",
-        reference = lambda wildcard: "config/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/config/reference_{serotype}_{gene}.gb"
+        reference = lambda wildcard: "defaults/reference_{serotype}_genome.gb" if wildcard.gene in ['genome'] else "results/defaults/reference_{serotype}_{gene}.gb"
     output:
         alignment = "results/{gene}/aligned_{serotype}.fasta"
     shell:

diff --git a/phylogenetic/rules/prepare_sequences_E.smk b/phylogenetic/rules/prepare_sequences_E.smk
@@ -21,10 +21,10 @@ rule generate_E_reference_files:
     Generating reference files for the E gene
     """
     input:
-        reference = "config/reference_{serotype}_genome.gb",
+        reference = "defaults/reference_{serotype}_genome.gb",
     output:
-        fasta = "results/config/reference_{serotype}_E.fasta",
-        genbank = "results/config/reference_{serotype}_E.gb",
+        fasta = "results/defaults/reference_{serotype}_E.fasta",
+        genbank = "results/defaults/reference_{serotype}_E.gb",
     params:
         gene = "E",
     shell:
@@ -42,7 +42,7 @@ rule align_and_extract_E:
     """
     input:
         sequences = "data/sequences_{serotype}.fasta",
-        reference = "results/config/reference_{serotype}_E.fasta"
+        reference = "results/defaults/reference_{serotype}_E.fasta"
     output:
         sequences = "results/E/sequences_{serotype}.fasta"
     params: