Renamed "config" to "defaults"

Based on discussion in nextstrain/pathogen-repo-guide#27.

Renaming "config" to "defaults" to prevent confusion with the new
"build-configs" directory to be in the following commit.

Conforms to the pathogen-repo-guide's new directory structure.
https://github.com/nextstrain/pathogen-repo-guide/tree/89b3c5dbc9b8f6a009f4a19c3ac56113bc5511ee

ingest/README.md

@@ -20,11 +20,11 @@ This produces a directory called `results` with the following files:
 - `sequences.fasta` - sequences in FASTA format
 - `metadata.tsv` - metadata in TSV format
 
-## Config
+## Defaults
 
-The config directory contains all of the default configurations for the ingest workflow.
+The defaults directory contains all of the default configurations for the ingest workflow.
 
-[config/defaults.yaml](config/defaults.yaml) contains all of the default configuration parameters
+[defaults/config.yaml](defaults/config.yaml) contains all of the default configuration parameters
 used for the ingest workflow. Use Snakemake's `--configfile`/`--config`
 options to override these default values.
 

ingest/Snakefile

@@ -6,7 +6,7 @@ and defines its default outputs.
 workdir: workflow.current_basedir
 
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
-configfile: "config/defaults.yaml"
+configfile: "defaults/config.yaml"
 
 
 include: "rules/fetch_from_ncbi.smk"

ingest/config/defaults.yaml → ingest/defaults/config.yaml

@@ -13,7 +13,7 @@ ncbi_dataset_fields: []
 # Config parameters related to the curate pipeline
 curate:
   geolocation_rules_url: "https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv"
-  local_geolocation_rules: "config/geolocation_rules.tsv"
+  local_geolocation_rules: "defaults/geolocation_rules.tsv"
   field_map:
     Source database: database
     Isolate Collection date: date
@@ -40,7 +40,7 @@ curate:
   authors_field: 'authors'
   authors_default_value: '?'
   abbr_authors_field: 'abbr_authors'
-  annotations: "config/annotations.tsv"
+  annotations: "defaults/annotations.tsv"
   annotations_id: 'accession'
   output_id_field: "accession"
   output_sequence_field: "sequence"

phylogenetic/README.md

@@ -19,11 +19,11 @@ desired data formatting and curations as part of the [ingest](../ingest/) workfl
 2. The `date` column in the metadata must be in ISO 8601 date format (i.e. YYYY-MM-DD).
 3. Ambiguous dates should be masked with `XX` (e.g. 2023-01-XX).
 
-## Config
+## Defaults
 
-The config directory contains all of the default configurations for the phylogenetic workflow.
+The defaults directory contains all of the default configurations for the phylogenetic workflow.
 
-[config/defaults.yaml](config/defaults.yaml) contains all of the default configuration parameters
+[defaults/config.yaml](defaults/config.yaml) contains all of the default configuration parameters
 used for the phylogenetic workflow. Use Snakemake's `--configfile`/`--config`
 options to override these default values.
 

phylogenetic/Snakefile

@@ -78,7 +78,7 @@ rule filter:
     input:
         sequences="data/sequences.fasta",
         metadata="data/metadata.tsv",
-        exclude="config/exclude.txt",
+        exclude="defaults/exclude.txt",
         index="data/sequences.index",
     output:
         sequences="builds/{build}/sequences.fasta",
@@ -103,8 +103,8 @@ rule filter:
 rule nextalign_before_mask:
     input:
         fasta="builds/{build}/sequences.fasta",
-        reference="config/reference.fasta",
-        genemap="config/genemap.gff",
+        reference="defaults/reference.fasta",
+        genemap="defaults/genemap.gff",
     output:
         alignment="builds/{build}/premask.fasta",
     shell:
@@ -136,8 +136,8 @@ rule mask:
 rule nextalign_after_mask:
     input:
         fasta="builds/{build}/masked.fasta",
-        reference="config/reference.fasta",
-        genemap="config/genemap.gff",
+        reference="defaults/reference.fasta",
+        genemap="defaults/genemap.gff",
     output:
         alignment="builds/{build}/aligned.fasta",
     params:
@@ -208,7 +208,7 @@ rule ancestral:
     input:
         tree="builds/{build}/tree.nwk",
         alignment="builds/{build}/premask.fasta",
-        annotation="config/reference.gb",
+        annotation="defaults/reference.gb",
     output:
         node_data="builds/{build}/muts.json",
     params:
@@ -234,7 +234,7 @@ rule clades:
     input:
         tree="builds/{build}/tree.nwk",
         node_data="builds/{build}/muts.json",
-        clades="config/clades.tsv",
+        clades="defaults/clades.tsv",
     output:
         clades="builds/{build}/clades.json",
     shell:
@@ -253,7 +253,7 @@ rule export:
         node_data="builds/{build}/branch_lengths.json",
         clades="builds/{build}/clades.json",
         ancestral="builds/{build}/muts.json",
-        auspice_config="config/auspice_config.json",
+        auspice_config="defaults/auspice_config.json",
         lat_longs=rules.download_lat_longs.output,
         metadata="builds/{build}/metadata.tsv",
     output: