modules icon indicating copy to clipboard operation
modules copied to clipboard

DRAFT: Add nanomonsv/parse code

Open awgymer opened this issue 3 years ago • 1 comments

Adding a new module for nanomonsv/parse. This is an SV caller for tumour/normal data from ONT sequencing.

I have opened a PR for new test data https://github.com/nf-core/test-datasets/pull/664

Tests are passing with docker and the data locally currently.

PR checklist

Closes #2319

  • [x] This comment contains a description of changes (with reason).
  • [x] If you've fixed a bug or added code that should be tested, add tests!
  • [x] If you've added a new tool - have you followed the module conventions in the contribution docs
  • [x] If necessary, include test data in your PR.
  • [x] Remove all TODO statements.
  • [x] Emit the versions.yml file.
  • [x] Follow the naming conventions.
  • [ ] Follow the parameters requirements.
  • [ ] Follow the input/output options guidelines.
  • [x] Add a resource label
  • [x] 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:
    • [x] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [x] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

awgymer avatar Oct 17 '22 15:10 awgymer

I need to update the path to the test-data. It currently points to my fork.

awgymer avatar Oct 17 '22 15:10 awgymer

@nf-core-bot fix linting

awgymer avatar Oct 18 '22 14:10 awgymer