Comments (6)
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
from avian-flu.
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': '?',
from avian-flu.
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/
.
from avian-flu.
Thanks for catching that @jameshadfield , not sure how I missed the subtype
field!
from avian-flu.
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.
from avian-flu.
Closed by #28 - can revisit uploads to S3 and merging with fauna in a future issue.
from avian-flu.
Related Issues (20)
- Ingest NCBI GenBank data for H5N1 outbreak HOT 7
- ingest: Upload NCBI/Andersen lab outputs to S3
- ingest: Join NCBI and Andersen lab data
- Automate ingest via GH Actions
- ingest: Run Nextclade as part of ingest HOT 2
- ingest/andersen-lab: Switch to automated CSV file HOT 1
- Add GH Action for phylogenetic workflows
- Reduce inference of unknown data/location for SRA sequences HOT 1
- ingest/ncbi: use new augur curate commands
- NCBI automation: connect ingest and phylogenetic workflows
- Snakemake improvements HOT 2
- Automated NCBI workflow not storing cache as expected
- NCBI/Andersen-lab: duplicate strain names HOT 3
- Adding USDA genotype and lineage
- Explore NCBI Assembly records to link segment sequences
- Not able to build / download data sets HOT 5
- Add `Snakefile.clades` rules into main snakefile
- Add fauna path to config HOT 1
- GenBank host name update
- NCBI ingest: reduce manual curation of hosts HOT 1
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from avian-flu.