Skip to content

Mixcr #8665

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
Open
wants to merge 9 commits into
base: master
Choose a base branch
from
Open

Mixcr #8665

wants to merge 9 commits into from

Conversation

derrik-gratz
Copy link

@derrik-gratz derrik-gratz commented Jun 17, 2025 •
edited
Loading

PR checklist

Init basic MiXCR module for TCR/BCR processing. While there is a lot more functionality in MiXCR that could be added for larger workflows (e.g. airrflow), for now this just includes MiXCR's catch-all wrapper analyze that will run the full tool. The CI framework set up here should allow easier addition & maintenance of additional MiXCR processes too, as the github secret workflow is set up.

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
    • MiXCR does not want their software hosted on bioconda for licensing concerns
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

derrik-gratz and others added 4 commits June 17, 2025 19:14
@derrik-gratz
Init MixCR (#8632)
a52de8b 
* init mixcr

* init test

* license as value to support github action workflows

* add mixcr license secret

* move license to secret, no input channel option

* rename process

* pre-lint

* make analyze subdir, prep for additional tools

* lint

* rename mixcr secret
@derrik-gratz
Patch 1 (#8661)
f29d4ad 
* bump snapshot with new container

* container to 4.7.0 base (no dev version)
@derrik-gratz
test
37bd233
@derrik-gratz
simplify snapshot
affbc72
@derrik-gratz derrik-gratz marked this pull request as draft June 17, 2025 21:11
@derrik-gratz derrik-gratz marked this pull request as ready for review June 18, 2025 00:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@derrik-gratz