Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Incorporate who mut cat in tbprofiler #253

Merged
merged 18 commits into from
Jan 10, 2024
Merged

Incorporate who mut cat in tbprofiler #253

merged 18 commits into from
Jan 10, 2024

Conversation

ryanjameskennedy
Copy link
Collaborator

@ryanjameskennedy ryanjameskennedy commented Jan 4, 2024 •
edited
Loading

Description

Summary of the changes made:

  • Added tbdb as submodule
  • Configs updated regarding mykrobe json to csv format
  • workflows/mycobaterium_tuberculosis.nf updated to run tbprofiler for WHO db and TBprofiler db
  • TEMPORARY: Remove Tbprofiler run using WHO database until TBProfiler issue 313 resolved.

Primary function of PR

  • Major functionality improvement / New type of analysis

Testing

Tested by running a tb test sample

@ryanjameskennedy ryanjameskennedy marked this pull request as draft January 4, 2024 14:24
@ryanjameskennedy ryanjameskennedy linked an issue Jan 4, 2024 that may be closed by this pull request
Mykrobe: csv output should be used #228
Closed
@ryanjameskennedy ryanjameskennedy marked this pull request as ready for review January 5, 2024 09:44
mhkc
mhkc approved these changes Jan 5, 2024
View reviewed changes
Copy link
Collaborator

@mhkc mhkc left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me!

@ryanjameskennedy ryanjameskennedy linked an issue Jan 5, 2024 that may be closed by this pull request
Mycobacterium tuberculosis: Add WHO mutation catalogue to TBprofiler #254
Closed
5 tasks
@ryanjameskennedy ryanjameskennedy merged commit 1288d88 into master Jan 10, 2024
1 check passed
@ryanjameskennedy ryanjameskennedy deleted the incorporate-who-mut-cat-in-tbprofiler branch April 22, 2024 08:40
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mhkc mhkc mhkc approved these changes

@sylvinite sylvinite Awaiting requested review from sylvinite

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Mycobacterium tuberculosis: Add WHO mutation catalogue to TBprofiler Mykrobe: csv output should be used
2 participants
@ryanjameskennedy @mhkc