From 08b15e6598b58ec4fcbc20f88bc7e283ee93ef91 Mon Sep 17 00:00:00 2001 From: John SJ Anderson Date: Fri, 9 Aug 2024 11:07:04 -0700 Subject: [PATCH] Add anchors used in other files/links [#1133] --- docs/src/reference/workflow-config-file.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/src/reference/workflow-config-file.rst b/docs/src/reference/workflow-config-file.rst index 8b29387cf..c347c4cc9 100644 --- a/docs/src/reference/workflow-config-file.rst +++ b/docs/src/reference/workflow-config-file.rst @@ -15,6 +15,8 @@ Primary configuration 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: + inputs ------ @@ -400,6 +402,7 @@ strip_strain_prefixes - description: A list of prefixes to strip from strain names in metadata and sequence records to maintain consistent strain names when analyzing data from multiple sources. - default: ``["hCoV-19/", "SARS-CoV-2/"]`` +.. _auspice_json_prefix: auspice_json_prefix ------------------- @@ -595,6 +598,8 @@ 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: + sanitize_metadata -----------------