Renamed "config" to "defaults"

Based on discussion in #27.

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

ingest/README.md

@@ -19,11 +19,11 @@ This produces a `results` directory with the following outputs:
 - sequences.fasta
 - metadata.tsv
 
-## 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

@@ -4,7 +4,7 @@ and defines its default outputs.
 """
 
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
-configfile: "config/defaults.yaml"
+configfile: "defaults/config.yaml"
 
 # This is the default rule that Snakemake will run when there are no specified targets.
 # The default output of the ingest workflow is usually the curated metadata and sequences.

nextclade/README.md

@@ -6,11 +6,11 @@ The new standard would be to include the Nextclade workflow within the pathogen
 This workflow is used to create the Nextclade datasets for this pathogen.
 All official Nextclade datasets are available at https://github.com/nextstrain/nextclade_data.
 
-## Config
+## Defaults
 
-The config directory contains all of the default configurations for the Nextclade workflow.
+The defaults directory contains all of the default configurations for the Nextclade 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 Nextclade workflow. Use Snakemake's `--configfile`/`--config`
 options to override these default values.
 

nextclade/Snakefile

@@ -4,7 +4,7 @@ a Nextclade dataset.
 """
 
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
-configfile: "config/defaults.yaml"
+configfile: "defaults/config.yaml"
 
 # This is the default rule that Snakemake will run when there are no specified targets.
 # The default output of the Nextclade workflow is usually the produced Nextclade dataset.

phylogenetic/README.md

@@ -13,11 +13,11 @@ 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

@@ -4,7 +4,7 @@ workflow and define its default output(s).
 """
 
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
-configfile: "config/defaults.yaml"
+configfile: "defaults/config.yaml"
 
 
 # This is the default rule that Snakemake will run when there are no specified targets.