feat(merquryfk/merquryfk): use topic versions and emit all images in single channel

[prototaxites]

A few changes here:

• merquryfk/merquryfk and merquryfk/hapmaker both use topic versions
• merquryfk/merquryfk emits the image files in a single output channel
• I fixed the tests for merquryfk/merquryfk, as it requires the outputs from merqury/hapmaker, and the channel joins in the old tests were also resulting in empty inputs. In doing this I discovered that in trio mode, there is some library loading issue that stops the test from completing. I've commented out the trio test in the mean time, and we can investigate if it is a data or a container issue at a later date.

edit: this appears to be a bug in merquryfk, it refers to a wrong file name internally. Not sure if it's been fixed as there hasn't been a new version tagged in a while...

    rm: error while loading shared libraries: libc.so.6: cannot open shared object file: Error 24
    Logex: Cannot open table test_mat
    MerquryFK: Command 'Logex -T2 -H1000 '._CN_PLT.1ZLS2M.0=B-A' '._CN_PLT.1ZLS2M.1=B&.A[1]' '._CN_PLT.1ZLS2M.2=B&.A[2]' '._CN_PLT.1ZLS2M.3=B&.A[3]' '._CN_PLT.1ZLS2M.4=B&.A[4]' '._CN_PLT.1ZLS2M.5=B&.A[5-]' '._CN_PLT.1ZLS2M.6=A-B' ._MQY_A1.xou5Lf test_mat' failed

edit2: Yes, this is a bug in the tagged version of merquryFK - I can run the command in .command.sh fine with the latest commit. I'll endeavour to get Gene to tag a release, but this might take some time or not be possible.

edit3: MerquryFK bumped to 1.2 and added a trio test dataset. Now the tests pass and the tool works correctly :)

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:
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    • 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

[charles-plessy]

It looks good to me but have some minor questions. Also, I do not have experience with this module, so I recommend to leave some time to others to comment before merging.

[prototaxites]

I tried bumping to the latest 1.1.3 release to see if it fixes the error with trio inputs, but no dice. So I'm happy to leave that disabled for now and to see if we can get the issue fixed later.

edit: I have found the bug and created a PR to fix it upstream, also: thegenemyers/MERQURY.FK#20

[prototaxites]

OK, I've spoken with the author and he is has written and will tag a fix for this bug. So I'll hold off on merging this PR until that's sorted and the new version is live, then incorporate that so we have a working module.

[prototaxites]

OK, almost there - this module needs some real trio test data as the test fails due to a floating point error. I'll add this to test-datasets, then we should be good to go.

[prototaxites]

nf-core/test-datasets#1841

[prototaxites]

OK, I think this is good to go! @mashehu, might you be able to force-merge again? 🙏 This one also suffers from the hidden: true linting issue.

[mashehu]

👍🏻 will wait for the tests to pass though

[prototaxites]

@mashehu And tests passing here 🙏

[mashehu]