Move ncbi taxon id to config #217
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
victorlin
approved these changes
Oct 30, 2023
joverlee521
approved these changes
Oct 30, 2023
There was a problem hiding this comment.
Thanks for keeping things up-to-date in monkeypox! Changes look good to me.
Consider if we should update the monkeypox description to point to the config file instead of hardcoding the taxon id. I don't think we will ever change the taxon id, but just in case they might get out of sync.
j23414
force-pushed
the
taxon_id_config
branch
from
c0c8049
to
3b45c7e
Compare
j23414
commented
Oct 30, 2023
| @@ -18,7 +18,7 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mon | |||
|
|
|||
| #### Underlying data | |||
| We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/), | |||
| using NCBI Taxonomy ID "10244", as starting point for these analyses. | |||
| using an NCBI Taxonomy ID defined in [ingest/config/config.yaml](https://github.com/nextstrain/monkeypox/blob/master/ingest/config/config.yaml), as starting point for these analyses. | |||
There was a problem hiding this comment.
I realized I could have submitted this as a separate PR. But would this wording be okay, @joverlee521 ?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Inspired by the following comment:
Related issue(s)
Checklist