Update FastK + MerquryFK versions + allow conda, add merquryfk/hapmaker module, port to nf-test

[prototaxites]

Apologies, this ended up being a much bigger PR than I first anticipated... seemed easier to roll everything into a single change than to do multiple PRs picking up little bits of this. All the changes are pretty similar across modules though.

• Updates FastK to version 1.1 (now in bioconda)
• Updates MerquryFK to version 1.1.1 (also now in bioconda)
  • Note that this requires pinning ggplot2 at >=3.4.0, <3.5.0
• Both these modules now have a conda option and share a single Seqera container
• Tidy all merquryfk output channels so that PNG and PDF are emitted from a single channel
• Port all tests to nf-test
• Add merquryfk/hapmaker module

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

[prototaxites]

OK, think this looks ready to go. The linting error looks like a bug in the linter - it's imagining an extra entry in one of the output tuples (ap_ktab). I've checked for e.g. hidden characters and the like and not spotted anything:

Module meta.yml does not match main.nf. Outputs should contain: {'mathap_ktab': ['meta', '${input_mat}.hap.ktab", hidden: true'], 'pathap_ktab': ['meta2', '${input_pat}.hap.ktab", hidden: true', 'ap_ktab'], 'versions': ['versions.yml']}

[itrujnara]

This is a massive amount of work, and the overall quality is quite good. I've left some improvement suggestions here and there.

[prototaxites]

Thanks for the review! I think I've addressed everything, but let me know if there's anything I've missed :)

[itrujnara]

Good job, no more issues from my side

[SPPearce]

Just to add, please split PRs like this up into individual chunks (i.e. one module at a time), it makes it much easier to review.