[docs] add explanation to config categories
As suggested by in review :)
@@ -5,10 +5,11 @@ Configuration parameters for Nextstrain SARS-CoV-2 workflow
:local:
:depth: 2
-Main Workflow configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Primary configuration
+^^^^^^^^^^^^^^^^^^^^^
-Parameters in this section define the main inputs and outputs of the workflow, as well as the important ``subsampling`` parameter. Often these will be the only parameters you need to modify.
+Parameters in this section define the main inputs and outputs of the workflow, as well as the commonly used ``subsampling`` rule.
+Often these will be the only parameters you need to modify.
inputs
------
@@ -345,9 +346,10 @@ priorities
hCoV-19/USA/CZB-3456/2021 -3.1
-Cross-Workflow configuration
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Secondary configuration
+^^^^^^^^^^^^^^^^^^^^^^^
+These parameters are other high-level parameters which may affect multiple Snakemake rules, or modify which rules are run.
default_build_name
------------------
@@ -554,6 +556,8 @@ emerging_lineages
Per-Rule configuration
^^^^^^^^^^^^^^^^^^^^^^
+Each top-level parameter here corresponds to a single Snakemake rule.
+Note that ``subsampling`` is a commonly used rule configuration which is described separately in the Primary configuration section.
sanitize_metadata
-----------------
@@ -1096,6 +1100,8 @@ group_by
Internal, Nextstrain-only configuration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+You shouldn't need to use parameters in this section unless you are running the core-Nextstrain builds. In addition to these parameters you will need AWS credentials set, e.g. in environment variables.
+
S3_DST_BUCKET
-------------
@@ -1143,8 +1149,10 @@ slack_token
- type: string
- description: `Slack authentication token <https://api.slack.com/authentication/token-types>`__ required for the Slack API calls to notify the defined ``slack_channel``. Only valid for Nextstrain builds.
-Miscellaneous
-^^^^^^^^^^^^^
+Unused Parameters
+^^^^^^^^^^^^^^^^^
+
+Documented here for completeness / historical accuracy.
partition_sequences
-------------------
