diff --git a/src/learn/parts.rst b/src/learn/parts.rst index 4a412361..43c3f2b9 100644 --- a/src/learn/parts.rst +++ b/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 `__, `Nextflow `__ and `WDL `__. A :term:`workflow` bundles one or more related :term:`builds` 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 `__, `Nextflow `__ +and `WDL `__. A :term:`workflow` can bundle one or more related +:term:`builds` which each produce a :term:`dataset` for visualization with :term:`Auspice`. -As an example, our core workflows are organized as `Git repositories `__ hosted on `GitHub `__. Each contains a :doc:`Snakemake workflow ` 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`. + +Our :term:`pathogen repositories` are organized as `Git repositories `__ +hosted on `GitHub `__. Each repository can contain +one or more workflows. .. graphviz:: :align: center @@ -176,7 +185,7 @@ As an example, our core workflows are organized as `Git repositories 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; } } diff --git a/src/reference/glossary.rst b/src/reference/glossary.rst index 780b7fb9..c02fb8ee 100644 --- a/src/reference/glossary.rst +++ b/src/reference/glossary.rst @@ -12,10 +12,16 @@ Glossary A web application used for phylogenetic visualization and analysis. :doc:`Documentation` + pathogen repository + + A version-controlled folder containing all files necessary to run a pathogen's :term:`workflows`. + workflow - also *pathogen workflow*, *pathogen analysis*, *Nextstrain workflow* + also *Nextstrain workflow* - A reproducible process comprised of one or more :term:`builds` producing :term:`datasets`, 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` producing outputs. + The outputs produced are often :term:`datasets`, 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` 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` 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` to run an analysis. :doc:`Documentation` + narrative A method of data-driven storytelling with interactive views of :term:`datasets ` displayed alongside multiple pages (or slides) of text and images. diff --git a/src/tutorials/creating-a-bacterial-pathogen-workflow.rst b/src/tutorials/creating-a-bacterial-pathogen-workflow.rst index 5d5747ee..1cf16938 100644 --- a/src/tutorials/creating-a-bacterial-pathogen-workflow.rst +++ b/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 diff --git a/src/tutorials/creating-a-workflow.rst b/src/tutorials/creating-a-workflow.rst index 77643af4..c3c2bb13 100644 --- a/src/tutorials/creating-a-workflow.rst +++ b/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 diff --git a/src/tutorials/running-a-workflow.rst b/src/tutorials/running-a-workflow.rst index 34d73bf9..5c5b5431 100644 --- a/src/tutorials/running-a-workflow.rst +++ b/src/tutorials/running-a-workflow.rst @@ -17,10 +17,10 @@ Prerequisites 1. :doc:`Install Nextstrain `. 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` are stored in :term:`workflow repositories` (version-controlled folders) to track changes over time. Download the `example Zika workflow repository `_. +:term:`Pathogen workflows` are stored in :term:`pathogen repositories` (version-controlled folders) to track changes over time. Download the `example Zika pathogen repository `_. .. code-block::