Add CI and example data

[victorlin]

Description of proposed changes

Generally inspired by existing practices in the monkeypox repo.

Related issue(s)

• Closes ENH: Add pathogen-ci to ci #27

Testing

• Checks pass

Post-merge

Add this repo to pathogen repo CI lists:

• Augur: Add nextstrain/rsv to CI augur#1274
• conda-base: Add nextstrain/rsv to CI conda-base#40
• docker-base: Add nextstrain/rsv to CI docker-base#174

[victorlin]

To reviewers: Does anyone know if there are filter options to better subsample the RSV data? The monkeypox filter includes the root and groups by clade + lineage. I'm not sure if those apply here.

[j23414]

Unfortunately I'm not seeing 'clade', 'lineage' or similar in the metadata:

$ head -n1 data/*/metadata.tsv                             
==> data/a/metadata.tsv <==
accession	genbank_accession_rev	strain	date	region	country	division	location	host	date_submitted	sra_accession	abbr_authors	reverse	authors	institution	F_coverage	G_coverage	genome_coverage

==> data/b/metadata.tsv <==
accession	genbank_accession_rev	strain	date	region	country	division	location	host	date_submitted	sra_accession	abbr_authors	reverse	authors	institution	F_coverage	G_coverage	genome_coverage

which would be required for the monkeypox-like filter. Clades aren't currently part of ingest rules, and doesn't happen until here in the build. Maybe a way forward is adding clade assignment in ingest but I would imagine this as a separate discussion and PR.

To get at your "better subsampling" question, maybe group by year and country? Similar to the rsv config file?

rsv/config/configfile.yaml

Lines 16 to 17 in ba171f4

	filter:
	group_by: "year country"

Others, feel free to chime in.

[victorlin]

Thanks, that's a good suggestion! Updated to use that config directly in 538442d.

[j23414]

Nice! LGTM :D

[victorlin]

Merging since this is already useful in #29.