Ingest Andersen Lab metadata and sequences about avian-flu

[joverlee521]

I tried to ensure that the metadata output from this workflow exactly matches @lmoncla 's metadata.

Currently there's just one difference in a strain name

A/Goose/USA/23-038138-001-original/2024->A/Goose/USA/23-038138-001-original/2023

[jameshadfield]

Nice work @joverlee521 - I ran this today with the following patch to simplify metadata merging and everything looks good

diff --git a/ingest/scripts/curate_andersen_lab_data.py b/ingest/scripts/curate_andersen_lab_data.py
index 4ded49e..a7b62d6 100644
--- a/ingest/scripts/curate_andersen_lab_data.py
+++ b/ingest/scripts/curate_andersen_lab_data.py
@@ -22,6 +22,7 @@ NEXTSTRAIN_RECORD = {
     'location': '?',
     'host': '?',
     'domestic_status': '?',
+    'subtype': 'h5n1',
     'originating_lab': '?',
     'submitting_lab': '?',
     'authors': '?',

[joverlee521]

WIP pushed up to https://github.com/nextstrain/avian-flu/tree/ingest-andersen-lab

Not hooked up to upload to S3 or merge/dedup with fauna data yet, but the ingest from the Andersen Lab's repo can be run with

nextstrain build ingest merge_andersen_segment_metadata 

This will output the results to ingest/results/andersen-lab/.

[joverlee521]

Thanks for catching that @jameshadfield , not sure how I missed the subtype field!

[joverlee521]

Based on internal discussion (Slack), holding off on uploading Andersen lab data to S3 and merging with fauna data since the current sequences have become available via GISAID.

Will make a PR to add the Andersen lab workflow to ingest/ in case we need to ingest any new data in the future.

[joverlee521]

Closed by #28 - can revisit uploads to S3 and merging with fauna in a future issue.