Add guide on filtering and subsampling

.gitignore

@@ -10,3 +10,4 @@ src/guides/bioinformatics/translate_ref.md
 src/guides/bioinformatics/vcf_input.md
 src/guides/communicate/create-pdf.md
 src/guides/communicate/narratives-intro.md
+src/snippets/filtering-and-subsampling.rst

src/conf.py

@@ -82,6 +82,8 @@
     'augur': ('https://docs.nextstrain.org/projects/augur/page/', None),
     'auspice': ('https://docs.nextstrain.org/projects/auspice/page/', None),
     'cli': ('https://docs.nextstrain.org/projects/cli/page/', None),
+    # For externally sourced snippets that reference this docs project
+    'docs.nextstrain.org': ('https://docs.nextstrain.org/page/', None),
     'nextclade': ('https://docs.nextstrain.org/projects/nextclade/page/', None),
     'ncov': ('https://docs.nextstrain.org/projects/ncov/page/', None)
 }

src/fetch-docs.py

@@ -22,6 +22,7 @@
     f'{augur_url}faq/fasta_input.md': 'guides/bioinformatics/fasta_input.md',
     f'{augur_url}faq/seq_traits.md': 'guides/bioinformatics/seq_traits.md',
     f'{augur_url}examples/examples.rst': 'guides/bioinformatics/examples.rst',
+    f'{augur_url}usage/cli/snippets/filtering-and-subsampling.rst': 'snippets/filtering-and-subsampling.rst',
 }
 
 if __name__ == '__main__':

src/guides/bioinformatics/filtering-and-subsampling.rst

@@ -0,0 +1,11 @@
+=========================
+Filtering and Subsampling
+=========================
+
+Below are some examples of using :doc:`augur filter <augur:usage/cli/filter>` to
+sample data.
+
+.. contents:: Table of Contents
+   :local:
+
+.. include:: ../../snippets/filtering-and-subsampling.rst

src/guides/bioinformatics/index.rst

@@ -10,11 +10,12 @@ How-to guides for performing bioinformatic anaylses with Nextstrain.
    :titlesonly:
    :caption: Table of contents
 
-   defining-clades
+   filtering-and-subsampling
    augur_snakemake
    missing-sequence-data
    translate_ref
    import-beast
+   defining-clades
    colors
    lat_longs
    vcf_input