Remove ndjson scripts from existing pathogen repos - Githubissues

nextstrain / ingest

Shared internal tooling for pathogen data ingest. Used by our pathogen build repos.

1 stars 0 forks source link

Remove ndjson scripts from existing pathogen repos #28

Open victorlin opened 8 months ago

victorlin commented 8 months ago

Follow-up to #1. Copying some useful text from the Google doc linked there:

csv-to-ndjson / tsv-to-ndjson

No longer needed as this can be done with augur curate passthru.

We can remove this script from the following repos (found with code search) as we update their workflows to use augur curate.

[ ] hepatitsB
[ ] monkeypox
[x] https://github.com/nextstrain/ncov-ingest/commit/6ef4dc097df037130845d002e54eb4b7338e3d5b
[ ] Rsv
[ ] Dengue (won't show up in code search as it's on a branch)
[ ] Zika and Ebola (won't show up in code search as it's on a branch)

fasta-to-ndjson

No longer needed as this can be done with a combination of augur parse and augur curate passthru.

We can remove this script from the following repos (found with code search) as we update their workflows.

[ ] monkeypox
[ ] Rsv
[ ] Dengue (won't show up in code search as it's on a branch)
[ ] Zika and Ebola (won't show up in code search as it's on a branch)

ndjson-to-tsv-and-fasta

No longer needed as this can be done with augur curate passthru.

We can remove this script from the following repos (found with code search) as we update their workflows.

[ ] monkeypox
[ ] Rsv
[ ] Dengue (won't show up in code search as it's on a branch)
[ ] Zika and Ebola (won't show up in code search as it's on a branch)

joverlee521 commented 1 week ago

I consider this slightly blocked by a bug in augur curate passthru.