Rename "profiles" to "build-configs"

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.
 
@@ -34,12 +34,12 @@ The modules of the workflow are in separate files to keep the main ingest [Snake
 Modules are all [included](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes)
 in the main Snakefile in the order that they are expected to run.
 
-## Profiles
+## Build configs
 
-The profiles directory contains custom configs and rules that override and/or
+The build-configs directory contains custom configs and rules that override and/or
 extend the default workflow.
 
-- [nextstrain_automation](profiles/nextstrain_automation/) - profile for the internal automated Nextstrain builds.
+- [nextstrain-automation](build-configs/nextstrain-automation/) - automated internal Nextstrain builds.
 
 
 ## Vendored

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.

ingest/profiles/nextstrain_automation/defaults.yaml → ingest/build-configs/nextstrain-automation/config.yaml

@@ -4,7 +4,7 @@
 # Custom rules to run as part of the Nextstrain automated workflow
 # The paths should be relative to the ingest directory.
 custom_rules:
-  - profiles/nextstrain_automation/upload.smk
+  - build-configs/nextstrain-automation/upload.smk
 
 # Nextstrain CloudFront domain to ensure that we invalidate CloudFront after the S3 uploads
 # This is required as long as we are using the AWS CLI for uploads

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.
 
@@ -20,3 +20,10 @@ The rules directory contains separate Snakefiles (`*.smk`) as modules of the cor
 The modules of the workflow are in separate files to keep the main ingest [Snakefile](Snakefile) succinct and organized.
 Modules are all [included](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes)
 in the main Snakefile in the order that they are expected to run.
+
+## Build configs
+
+The build-configs directory contains custom configs and rules that override and/or
+extend the default workflow.
+
+- [test-dataset](build-configs/test-dataset/) - build to test new Nextclade dataset

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.

nextclade/profiles/test_dataset/defaults.yaml → nextclade/build-configs/test-dataset/config.yaml

@@ -4,4 +4,4 @@
 # Custom rules to run as part of the testing workflow
 # The paths should be relative to the phylogenetic directory.
 custom_rules:
-  - profiles/test_dataset/test_dataset.smk
+  - build-configs/test-dataset/test_dataset.smk

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.
 
@@ -28,11 +28,11 @@ The modules of the workflow are in separate files to keep the main ingest [Snake
 Modules are all [included](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#includes)
 in the main Snakefile in the order that they are expected to run.
 
-## Profiles
+## Build configs
 
-The profiles directory contains custom configs and rules that override and/or
+The build-configs directory contains custom configs and rules that override and/or
 extend the default workflow.
 
-- [ci](profiles/ci/) - profile for the CI build that runs with example data
+- [ci](build-configs/ci/) - CI build that runs with example data
 
 [Nextstrain datasets]: https://docs.nextstrain.org/en/latest/reference/glossary.html#term-dataset

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.

phylogenetic/profiles/ci/defaults.yaml → phylogenetic/build-configs/ci/config.yaml

@@ -4,4 +4,4 @@
 # Custom rules to run as part of the CI automated workflow
 # The paths should be relative to the phylogenetic directory.
 custom_rules:
-  - profiles/ci/copy_example_data.smk
+  - build-configs/ci/copy_example_data.smk