Skip to content

Topics for a bunch of SV related modules#10113

Merged
nvnieuwk merged 10 commits intonf-core:masterfrom
nvnieuwk:topics/sv-modules
Feb 23, 2026
Merged

Topics for a bunch of SV related modules#10113
nvnieuwk merged 10 commits intonf-core:masterfrom
nvnieuwk:topics/sv-modules

Conversation

@nvnieuwk
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.
  • 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

Copy link
Contributor

@Joon-Klaps Joon-Klaps left a comment

Choose a reason for hiding this comment

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

Dunno why you have in your tests a versions_ if this wasn't intentional, double check if it was, LGTM!

{ assert snapshot(
file(process.out.npz[0][1]).name,
process.out.versions
process.out.findAll { it.key.startsWith("versions_") }
Copy link
Contributor

Choose a reason for hiding this comment

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

why a _?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Ah it's the same as versions, the emit is always versions_<tool> so it just does the same thing :)

{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { it.key.startsWith("versions_") },
Copy link
Contributor

Choose a reason for hiding this comment

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

again why a _

{ assert process.success },
{ assert snapshot(
process.out.versions,
process.out.findAll { it.key.startsWith("versions_") },
Copy link
Contributor

Choose a reason for hiding this comment

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

did you mess up ur global replace?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

I guess I manually typed these 😁 they're similar in funcionality as you can see in the snapshot

@nvnieuwk nvnieuwk added this pull request to the merge queue Feb 23, 2026
Merged via the queue into nf-core:master with commit fdcc397 Feb 23, 2026
72 checks passed
@nvnieuwk nvnieuwk deleted the topics/sv-modules branch February 23, 2026 08:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants