diff --git a/ingest/README.md b/ingest/README.md
index 1713cea..4ed0fa3 100644
--- a/ingest/README.md
+++ b/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.
 
diff --git a/ingest/Snakefile b/ingest/Snakefile
index 6bf5b5b..65e8fca 100644
--- a/ingest/Snakefile
+++ b/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.
diff --git a/ingest/config/annotations.tsv b/ingest/defaults/annotations.tsv
similarity index 100%
rename from ingest/config/annotations.tsv
rename to ingest/defaults/annotations.tsv
diff --git a/ingest/config/defaults.yaml b/ingest/defaults/config.yaml
similarity index 100%
rename from ingest/config/defaults.yaml
rename to ingest/defaults/config.yaml
diff --git a/ingest/config/geolocation_rules.tsv b/ingest/defaults/geolocation_rules.tsv
similarity index 100%
rename from ingest/config/geolocation_rules.tsv
rename to ingest/defaults/geolocation_rules.tsv
diff --git a/ingest/config/nextclade_field_map.tsv b/ingest/defaults/nextclade_field_map.tsv
similarity index 100%
rename from ingest/config/nextclade_field_map.tsv
rename to ingest/defaults/nextclade_field_map.tsv
diff --git a/nextclade/README.md b/nextclade/README.md
index f9da746..59a711f 100644
--- a/nextclade/README.md
+++ b/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.
 
diff --git a/nextclade/Snakefile b/nextclade/Snakefile
index 0dce54c..8cb429d 100644
--- a/nextclade/Snakefile
+++ b/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.
diff --git a/nextclade/config/defaults.yaml b/nextclade/defaults/config.yaml
similarity index 100%
rename from nextclade/config/defaults.yaml
rename to nextclade/defaults/config.yaml
diff --git a/phylogenetic/README.md b/phylogenetic/README.md
index b1c7d5a..05e9c8a 100644
--- a/phylogenetic/README.md
+++ b/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.
 
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
index 2b33d2f..d038c47 100644
--- a/phylogenetic/Snakefile
+++ b/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.
diff --git a/phylogenetic/config/defaults.yaml b/phylogenetic/defaults/config.yaml
similarity index 100%
rename from phylogenetic/config/defaults.yaml
rename to phylogenetic/defaults/config.yaml