8000 Bgzip and tabix stranger by fellen31 · Pull Request #8509 · nf-core/modules · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Bgzip and tabix stranger #8509

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
Merged
merged 5 commits into from
May 19, 2025
Merged

Bgzip and tabix stranger #8509

merged 5 commits into from
May 19, 2025

Conversation

fellen31
Copy link
Contributor

PR checklist

Closes #XXX

  • 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.
  • 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
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@fellen31 fellen31 requested a review from ramprasadn May 19, 2025 14:37
JoseEspinosa
JoseEspinosa reviewed May 19, 2025
View reviewed changes
Copy link
Member
@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

Is there already a tabix module, so I'd say that this addition is against this guideline

@fellen31
Copy link
Contributor Author

Is there already a tabix module, so I'd say that this addition is against this guideline

Thought this was OK from other PRs:

I'd argue in this case since the index is so tightly linked with the compressed VCF, it's easier to have a multi-tool module rather than to have a subworkflow with this module emitting a gzipped file, then another module un-compressing, bgzipping and indexing.

JoseEspinosa
JoseEspinosa approved these changes May 19, 2025
View reviewed changes
Copy link
Member
@JoseEspinosa JoseEspinosa left a comment

Choose a reason for hiding this comment

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

OK, fair enough, yes probably this fits well with https://nf-co.re/docs/guidelines/components/modules#compression-of-input-and-output-files
LGTM 🚀

@fellen31 fellen31 added this pull request to the merge queue May 19, 2025
Merged via the queue into nf-core:master with commit ffe458c May 19, 2025
24 checks passed
@fellen31 fellen31 deleted the tabix-stranger branch May 19, 2025 17:05
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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

Successfully merging this pull request may close these issues.
2 participants
@fellen31 @JoseEspinosa
0