Added stub and nf-test for merquryfk/merquryfk

[GallVp]

PR checklist

Closes #XXX

• [x] Added stub and nf-test for merquryfk/merquryfk
• [ ] 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
• [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:
  • For modules:
    • [x] 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

[GallVp]

Hi @mahesh-panchal

FASTK is running out of memory. Any suggestions? Thank you!

[mahesh-panchal]

I have no idea really. Best ask on nf-core.

I see also that some of the process selectors aren't matched, but I don't think that has anything to do with it.

[GallVp]

Thank you @mahesh-panchal and @famosab for the feedback

MERQURY.FK is not a well maintained tool. Even if we find out and fix this FASTK segmentation issue, it does not work in trio mode. I have tested that elsewhere. As suggested by @mahesh-panchal slack post, I agree we should be using MERQURY itself. See PR: https://github.com/nf-core/modules/pull/5657

I would like to close this PR.

[famosab]

@GallVp I think you'll need to deprecate the module (https://nf-co.re/docs/contributing/modules#deprecating-a-module) then and create an issue for a new one. But that seems sensible to me.

[mahesh-panchal]

I agree with deprecating this module too. It's kind of a shame, because the speed up and memory profile were much better, but really it would have been nicer if that was contributed directly back to the Merqury rather than a new unversioned unmaintained tool made. It was also nice that KATGC and SMUDGEPLOT were bundled here too.

[GallVp]

Good idea. But deprecating the module requires going through the CI, which is failing?

[mahesh-panchal]

True. Closing then seems the best. I'm still not sure what the issue is with the self hosted runners but they're not set up in the same way as Githubs.