Add table of contents to config reference
One top-level contents directive
Full contents directive for each top-level YAML section
Configuration parameters for Nextstrain SARS-CoV-2 workflow
===========================================================
+.. contents:: Table of Contents
+ :local:
+ :depth: 1
+
S3_DST_BUCKET
-------------
@@ -92,6 +96,9 @@ builds
Builds support any named attributes that can be referenced by subsampling schemes. Builds also support the following specific attributes.
+.. contents::
+ :local:
+
auspice_config
~~~~~~~~~~~~~~
@@ -177,6 +184,9 @@ files
- type: object
- description: Additional files used to configure tools used by the workflow (e.g., alignment references, names of strains to exclude during filtering, etc.).
+.. contents::
+ :local:
+
include
~~~~~~~
@@ -277,6 +287,9 @@ filter
- type: object
- description: Filters to apply to strain metadata and sequences prior to subsampling and tree inference. The workflow applies an implicit filter on the maximum collection dates later than today.
+.. contents::
+ :local:
+
min_length
~~~~~~~~~~
@@ -321,6 +334,9 @@ skip_diagnostics
frequencies
-----------
+.. contents::
+ :local:
+
.. _min_date-1:
min_date
@@ -430,6 +446,9 @@ inputs
Valid attributes for list entries in ``inputs`` are provided below.
+.. contents::
+ :local:
+
name
~~~~
@@ -496,6 +515,9 @@ logistic_growth
- ``min_frequency``
- ``max_frequency``
+.. contents::
+ :local:
+
delta_pivots
~~~~~~~~~~~~
@@ -535,6 +557,9 @@ mask
- ``mask_from_end``
- ``mask_sites``
+.. contents::
+ :local:
+
mask_from_beginning
~~~~~~~~~~~~~~~~~~~
@@ -581,6 +606,9 @@ refine
- ``divergence_unit``
- ``clock_filter_iqd``
+.. contents::
+ :local:
+
root
~~~~
@@ -701,6 +729,9 @@ sanitize_metadata
- type: object
- description: Parameters to configure how to sanitize metadata to a Nextstrain-compatible format. The sanitize metadata script resolves duplicate records using database ids, parses a GISAID-style location field into Nextstrain-style location fields, strips prefixes from strain names, and renames fields in that order.
+.. contents::
+ :local:
+
metadata_id_columns
~~~~~~~~~~~~~~~~~~~
@@ -781,6 +812,9 @@ subsampling
Each named subsampling scheme supports the following attributes that the workflow passes to ``augur filter``.
+.. contents::
+ :local:
+
group_by
~~~~~~~~
@@ -959,6 +993,9 @@ cluster
- type: object
- description: Parameters for clustering of closely related strains
+.. contents::
+ :local:
+
.. _min_tips-1:
min_tips
@@ -998,6 +1035,9 @@ traits
Each named traits configuration (``default`` or build-named) supports the following attributes.
+.. contents::
+ :local:
+
sampling_bias_correction
~~~~~~~~~~~~~~~~~~~~~~~~
