feat: hisat3n/build module

[emmcauley]

PR checklist

Closes #9667. Adds hisat3n/build, a tool that builds a 3N-index (containing two hisat2 indexes), from a set of DNA sequences. Tests includes --base-change in nextflow.config ext.args.

• 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

[SPPearce]

I suspect the version command could be shortened using sed to do both the grep and the cut

Suggested change

	tuple val("${task.process}"), val('hisat-3n'), eval("hisat-3n --version 2>&1 | grep -o 'version [^ ]*' | cut -d ' ' -f 2"), topic: versions, emit: versions_hisat3n_build
	tuple val("${task.process}"), val('hisat-3n'), eval("hisat-3n --version 2>&1 | grep -o 'version [^ ]*' | cut -d ' ' -f 2"), topic: versions, emit: versions_hisat3n

[emmcauley]

I'll be adding another module after this called hisat3n_align, which is why I was trying to differentiate -- given that context, does it still make sense to shorten the name?

[SPPearce]

The emit versions_ is only used for testing actually, if nf-test was able to directly test the topic channel we wouldn't bother with it at all.

[SPPearce]

All samtools tools use versions_samtools for instance

[SPPearce]

The linting is complaing about something with the command. I would try using single quotes in the eval (double quotes in the sed), and then it might be happier.
Other than that I'm happy to merge

[SPPearce]

You need to update your branch, unrelated changes are now failing.