Update glossary and graphviz for repo/workflows

With the push for pathogen repos to adhere to the pathogen-repo-guide,
the glossary and graphviz for repositories and workflows need to be
updated.

This will also make it easier to use standardized terminology in the
upcoming ingest tutorials.

src/learn/parts.rst

@@ -165,9 +165,18 @@ colloquially because they use a generic data format called JSON.
         metadata -> filter;
     }
 
-Builds run several commands and are often automated by workflow managers such as `Snakemake <https://snakemake.readthedocs.io>`__, `Nextflow <https://nextflow.io>`__ and `WDL <https://openwdl.org>`__. A :term:`workflow` bundles one or more related :term:`builds<build>` which each produce a :term:`dataset` for visualization with :term:`Auspice`.
+Builds run several commands and are often automated by workflow managers such as
+`Snakemake <https://snakemake.readthedocs.io>`__, `Nextflow <https://nextflow.io>`__
+and `WDL <https://openwdl.org>`__. A :term:`workflow` can bundle one or more related
+:term:`builds<build>` which each produce a :term:`dataset` for visualization with :term:`Auspice`.
 
-As an example, our core workflows are organized as `Git repositories <https://git-scm.com>`__ hosted on `GitHub <https://github.com/nextstrain>`__. Each contains a :doc:`Snakemake workflow </guides/bioinformatics/augur_snakemake>` using Augur, configuration, and data.
+A workflow can also produce outputs that are not limited to Auspice datasets. For example,
+ingest workflows produce curated metadata and sequences files and Nextclade workflows
+produce :term:`Nextclade datasets<Nextclade dataset>`.
+
+Our :term:`pathogen repositories<pathogen repository>` are organized as `Git repositories <https://git-scm.com>`__
+hosted on `GitHub <https://github.com/nextstrain>`__. Each repository can contain
+one or more workflows.
 
 .. graphviz::
     :align: center
@@ -176,44 +185,96 @@ As an example, our core workflows are organized as `Git repositories <https://gi
         graph [
             fontname="Lato, 'Helvetica Neue', sans-serif",
             fontsize=12,
-        ]
+        ];
         node [
             shape=box,
             style="rounded, filled",
             fontname="Lato, 'Helvetica Neue', sans-serif",
             fontsize=12,
             height=0.1,
             colorscheme=paired10,
+            pad=0.1,
+            margin=0.1,
         ];
-        rankdir=LR
+        rankdir=LR;
+
+        subgraph cluster_ncov {
+            label = "SARS-CoV-2 repository";
+            subgraph cluster_ncov_phylo {
+                label = "Phylogenetic workflow";
+                build0 [width=1, label="Global build"];
+                build1 [width=1, label="Africa build"];
+                build2 [width=1, label="Europe build"];
+                output0 [width=1, label="dataset"];
+                output1 [width=1, label="dataset"];
+                output2 [width=1, label="dataset"];
+                ellipses1 [width=1, label="...", penwidth=0, fillcolor="white"];
+                ellipses2 [width=1, label="...", penwidth=0, fillcolor="white"];
+            }
+        }
 
-        subgraph cluster_0 {
-            label = "Zika workflow";
-            build0 [width=1, label="Zika build"]
-            dataset0 [width=1, label="dataset"]
+        subgraph cluster_zika {
+            label = "Zika repository";
+            nojustify = true;
+            subgraph cluster_zika_ingest {
+                label = "Ingest workflow";
+                build3 [width=1, label="ingest build"];
+                output3 [width=1, label="output files"];
+            }
+            subgraph cluster_zika_phylo {
+                label = "Phylogenetic workflow";
+                build4 [width=1, label="phylogenetic build"];
+                output4 [width=1, label="dataset"];
+            }
         }
 
-        subgraph cluster_1 {
-            label = "SARS-CoV-2 workflow";
-            build1 [width=1, label="Global build"]
-            build2 [width=1, label="Africa build"]
-            build3 [width=1, label="Europe build"]
-            dataset1 [width=1, label="dataset"]
-            dataset2 [width=1, label="dataset"]
-            dataset3 [width=1, label="dataset"]
-            ellipses1 [width=1, label="...", penwidth=0, fillcolor="white"]
-            ellipses2 [width=1, label="...", penwidth=0, fillcolor="white"]
+        subgraph cluster_mpox {
+            label = "Mpox repository";
+            subgraph cluster_mpox_ingest {
+                label = "Ingest workflow";
+                build5 [width=1, label="ingest build"];
+                output5 [width=1, label="output files"];
+            }
+            subgraph cluster_mpox_phylo {
+                label = "Phylogenetic workflow";
+                build6 [width=1, label="mpxv build"];
+                build7 [width=1, label="hmpxv1 build"];
+                build8 [width=1, label="hmpxv1_big build"];
+                output6 [width=1, label="dataset"];
+                output7 [width=1, label="dataset"];
+                output8 [width=1, label="dataset"];
+
+            }
+            subgraph cluster_mpox_nextclade {
+                label = "Nextclade workflow";
+                build9 [width=1, label="all-clades build"];
+                build10 [width=1, label="clade-iib build"];
+                build11 [width=1, label="lineage-b.1 build"];
+                output9 [width=1, label="nextclade dataset"];
+                output10 [width=1, label="nextclade dataset"];
+                output11 [width=1, label="nextclade dataset"];
+
+            }
         }
 
-        build0 -> dataset0
-        build1 -> dataset1
-        build2 -> dataset2
-        build3 -> dataset3
+        build0 -> output0;
+        build1 -> output1;
+        build2 -> output2;
+        build3 -> output3;
+        build4 -> output4;
+        build5 -> output5;
+        build6 -> output6;
+        build7 -> output7;
+        build8 -> output8;
+        build9 -> output9;
+        build10 -> output10;
+        build11 -> output11;
 
         {
-            edge[style=invis]
-            dataset0 -> build1      // arrange clusters on same row
-            ellipses1 -> ellipses2
+            edge[style=invis];
+            output0 -> build3; // arrange clusters on same row
+            output3 -> build5; // arrange clusters on same row
+            ellipses1 -> ellipses2;
         }
     }
 

src/reference/glossary.rst

@@ -12,10 +12,16 @@ Glossary
 
       A web application used for phylogenetic visualization and analysis. :doc:`Documentation<auspice:index>`
 
+   pathogen repository
+
+      A version-controlled folder containing all files necessary to run a pathogen's :term:`workflows<workflow>`.
+
    workflow
-      also *pathogen workflow*, *pathogen analysis*, *Nextstrain workflow*
+      also *Nextstrain workflow*
 
-      A reproducible process comprised of one or more :term:`builds<build>` producing :term:`datasets<dataset>`, which can be visualized by :term:`Auspice`. Implementation varies per workflow, but generally they are run by workflow managers such as Snakemake.
+      A reproducible process comprised of one or more :term:`builds<build>` producing outputs.
+      The outputs produced are often :term:`datasets<dataset>`, which can be visualized by :term:`Auspice`.
+      Implementation varies per workflow, but generally they are run by workflow managers such as Snakemake.
 
       Our :term:`core workflows<core workflow>` can be divided into two types:
 
@@ -30,15 +36,11 @@ Glossary
 
       A :term:`workflow` maintained by the Nextstrain team.
 
-   workflow repository
-      also *pathogen workflow repository*
-
-      A version-controlled folder containing all files necessary to run a :term:`workflow`.
-
    build
       also *Nextstrain build*
 
-      *(noun)* A sequence of commands, parameters and input files which work together to reproducibly execute bioinformatic analyses and generate a :term:`dataset` for visualization with :term:`Auspice`.
+      *(noun)* A sequence of commands, parameters and input files which work together to reproducibly generate outputs.
+      Phylogenetic builds execute bioinformatic analyses and generate a :term:`dataset` for visualization with :term:`Auspice`.
 
    build (verb)
 
@@ -60,6 +62,10 @@ Glossary
 
       Some :term:`workflows<workflow>` produce a single, synonymous dataset, like Zika. Others, like seasonal flu, produce many datasets.
 
+   Nextclade dataset
+
+      A collection of input data files required for :doc:`Nextclade<nextclade:index>` to run an analysis. :doc:`Documentation<nextclade:user/datasets>`
+
    narrative
 
       A method of data-driven storytelling with interactive views of :term:`datasets <dataset>` displayed alongside multiple pages (or slides) of text and images.

src/tutorials/creating-a-bacterial-pathogen-workflow.rst

@@ -17,7 +17,7 @@ Prerequisites
 Setup
 =====
 
-1. Download the example :term:`workflow repository` and enter the new directory.
+1. Download the example :term:`pathogen repository` and enter the new directory.
 
    .. code-block:: bash
 

src/tutorials/creating-a-workflow.rst

@@ -21,7 +21,7 @@ Prerequisites
 Setup
 =====
 
-1. Change directory to the Zika :term:`workflow repository` downloaded in the previous tutorial.
+1. Change directory to the Zika :term:`pathogen repository` downloaded in the previous tutorial.
 
    .. code-block:: bash
 

src/tutorials/running-a-workflow.rst

@@ -17,10 +17,10 @@ Prerequisites
 
 1. :doc:`Install Nextstrain </install>`. These instructions will install all of the software you need to complete this tutorial and others.
 
-Download the example Zika workflow repository
+Download the example Zika pathogen repository
 =============================================
 
-:term:`Pathogen workflows<workflow>` are stored in :term:`workflow repositories<workflow repository>` (version-controlled folders) to track changes over time. Download the `example Zika workflow repository <https://github.com/nextstrain/zika-tutorial>`_.
+:term:`Pathogen workflows<workflow>` are stored in :term:`pathogen repositories<pathogen repository>` (version-controlled folders) to track changes over time. Download the `example Zika pathogen repository <https://github.com/nextstrain/zika-tutorial>`_.
 
 .. code-block::