Skip to content

feat: parsnp module#11196

Open
emmcauley wants to merge 7 commits intonf-core:masterfrom
fulcrumgenomics:em_parsnp_module
Open

feat: parsnp module#11196
emmcauley wants to merge 7 commits intonf-core:masterfrom
fulcrumgenomics:em_parsnp_module

Conversation

@emmcauley
Copy link
Copy Markdown
Contributor

PR checklist

Closes #8614.

This PR adds a new parsnp module and tests. The test is a bit contrived because I'm using the same FASTA files but I think it is sufficient -- I can also add some more complex test cases if preferred.

  • 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.
  • Broadcast software version numbers to topic: versions - See version_topics
  • 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

@emmcauley emmcauley marked this pull request as ready for review April 15, 2026 15:23
@emmcauley emmcauley added the new module Adding a new module label Apr 15, 2026
Copy link
Copy Markdown
Contributor

@akaviaLab akaviaLab left a comment

Choose a reason for hiding this comment

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

In general, looks good to me, but I have some comments. I'd suggest getting one of the core maintainers to look at it.

Comment thread modules/nf-core/parsnp/tests/main.nf.test Outdated
Comment thread modules/nf-core/parsnp/tests/main.nf.test Outdated
Copy link
Copy Markdown
Contributor

@famosab famosab left a comment

Choose a reason for hiding this comment

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

Thank you for your contribution to nf-core! I added a few comments to your PR. :)

Comment thread modules/nf-core/parsnp/main.nf Outdated
Comment thread modules/nf-core/parsnp/main.nf
Comment thread modules/nf-core/parsnp/main.nf Outdated
Comment thread modules/nf-core/parsnp/main.nf
Comment thread modules/nf-core/parsnp/meta.yml
@akaviaLab
Copy link
Copy Markdown
Contributor

akaviaLab commented Apr 22, 2026 via email

Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/meta.yml Outdated
Comment thread modules/nf-core/parsnp/tests/main.nf.test Outdated
@emmcauley emmcauley requested a review from famosab April 25, 2026 15:17
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

new module Adding a new module

Projects

None yet

Development

Successfully merging this pull request may close these issues.

new module: PARSNP

3 participants