initial commit of kma_index

[Krannich479]

PR checklist

Closes #7235

• 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

[famosab]

Looks good already :)

[Krannich479]

Great catch @famosab ! I was never really satisfied with my solutions for output and prefix. After reading your comments, I first thought of creating four output channels, one for each file, because my style of [val(meta), "${meta.id}.kmaindex.*"] output might even violates the nf-core output format specification of one output channel per file (my 'db' output channel emits four files in my current state).
Then I looked into what bwa index does and I think it's a very elegant solution:

1. def prefix takes the input file's baseName
2. bwa index creates a subdirectory for all index files
3. The module BWA_INDEX then emits only one channel ("index") which contains the subdirectory

I'd re-design the my KMA_INDEX module that way. What do you think?

[SPPearce]

Yes, I think that is the standard method to deal with index generation. The individual files on their own are useless, they are required in combination.

[Krannich479]

Docker test succeeds in gitpod.

[Krannich479]

@jfy133 is this the kind of proof you proposed?