Fixes for Andersen lab #56
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
Saw a series of warning messages from seqkit in recent ingest run that flagged spaces in strain names.¹ This results in the sequences being skipped during the merging of the two data sources. We could use the `--by-name` option for seqkit as the warning message suggested, but this reminded me that we do not support spaces in the strain name in our downstream phylogenetic analysis anyways. So just remove spaces from the strain name. ¹ https://github.com/nextstrain/avian-flu/actions/runs/9456655781/job/26048985198#step:13:1469
genehack
approved these changes
Jun 11, 2024
|
Looks great. Thank you! |
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Outdated suggestions cannot be applied.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
sra-via-andersen-labSee commits for details.
Related issue(s)
Follow up on #50 + #54
Checklist