Pangolin 4.0 compatability #1660
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
Recently pangolin has been updated to version 4.0 and this changes the output CSV file - see: https://github.com/cov-lineages/pangolin/releases/tag/v4.0 This causes the module to fail in its current state as row['qc_status'] already exists and the current replacement triggers a key error by searching for row['status'] which no longer exists. Thanks to @alexomics for tracking down the issue.
|
Thanks @mattloose! Do you have an example output file that we can add to ewels/MultiQC_TestData please? Then I can test locally as well.. |
|
I've created a table pangolin_4-0.csv from the example output table |
ewels
added a commit
to MultiQC/test-data
that referenced
this pull request
Apr 4, 2022
|
Great stuff, thanks! |
|
I see you have managed to find a CSV before I was able to reply. Glad this is resolved. Thanks. |
vladsavelyev
pushed a commit
to vladsavelyev/MultiQC_TestData
that referenced
this pull request
Apr 16, 2022
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Outdated suggestions cannot be applied.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.
Recently pangolin has been updated to version 4.0 and this changes the output CSV file - see: https://github.com/cov-lineages/pangolin/releases/tag/v4.0
This causes the module to fail in its current state as
row['qc_status']already exists and the current replacement triggers a key error by searching forrow['status']which no longer exists. Thanks to @alexomics for tracking down the issue.CHANGELOG.mdhas been updated