New module: hostile/clean

[jfy133]

NOT YET WORKING DUE TO A BUG IN THE TOOL ITSELF MISUNDERSTANDING OF DOCS

Need to either:

- Specifically specify the aligner for SE data
- Add error check if single end data that contents of index is actually minimaps2 compatible

Can be finished once bede/hostile#46 addressed

I still haven't done the meta.yml yet

Note: the two FASTQ files in the paired test are expected to be empty as all SARS-Cov2 reads aligned against the SARS-Cov2 reference genome (unsurprisingly ). Only a single read in the single-end data aligns for some reason.

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!
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[jfy133]

@nf-core-bot fix linting

[bede]

Hi James, thanks for contributing this module and please let me know if I can assist.

NOT YET WORKING DUE TO A BUG IN THE TOOL ITSELF

As discussed in bede/hostile#46, Hostile is working as expected here, although I understand how confusion has arisen, and will look into clarifying the usage section and error message generated when a custom index is passed in an unexpected format.

Thanks,
Bede

[jfy133]

Hi James, thanks for contributing this module and please let me know if I can assist.

NOT YET WORKING DUE TO A BUG IN THE TOOL ITSELF

As discussed in bede/hostile#46, Hostile is working as expected here, although I understand how confusion has arisen, and will look into clarifying the usage section and error message generated when a custom index is passed in an unexpected format.

Thanks, Bede

I think I've got it for now thanks @bede !

I considered adding extra checks myself but it's always better for this to happen upstream in this context :)

You can of course look at the code now and shout if you have any questiosn/suggestions for improvement