Add tmb module

[georgiakes]

PR checklist

Module for the tmb tool

• 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

[georgiakes]

Even though I run
nf-core modules lint tmb/pytmb --fix
The linting error still persists but I'm not sure why.

[maxulysse]

Even though I run nf-core modules lint tmb/pytmb --fix The linting error still persists but I'm not sure why.

I think you need to run it with the dev version

[georgiakes]

Still the same :(

[SPPearce]

We've had a discussion in the past about including small test files like these yml files in the tests folder; personally I think it is a good idea but it was not in consensus.
You can make this kind of file on the fly inside the nf-test though, like this: https://github.com/nf-core/modules/blob/master/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test#L58

[georgiakes]

We've had a discussion in the past about including small test files like these yml files in the tests folder; personally I think it is a good idea but it was not in consensus. You can make this kind of file on the fly inside the nf-test though, like this: https://github.com/nf-core/modules/blob/master/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test#L58

I'm not sure I completely understand, but the creation of the yml files are not created by another module and that is why I've included them on the tests folder.

[SPPearce]

The consensus seems to be not to allow these kind of files still.
You can create them inside nf-test though, like:

setup {
    new File("${launchDir}/test.yaml").text = """
        freq: "AF"
        depth: "DP"
        altDepth: "AD"
        maxVaf: "1"
""".stripIndent()
}

//...

process {
    """
    input[N] = file("${launchDir}/test.yaml")
    """
}

That'll work for the haplotc.yml, but the snpeff.yml is quite large.
The other option is to add them to the test-datasets repository, where all the other test data files live.