Added support for Cleanifier tool: cleanifier/download, cleanifier/index and cleanifier/filter

[LeonHornich]

With this PR I want to add support for the Cleanifier tool for species contamination removal. There are 3 added modules: download, index and filter.

Unfortunately I am still experiencing some issues with nf-test snapshot stability. If anyone has an idea on how to fix them i'd very much appreciate that. Of course other feedback is also highly appreciated.

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:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda

[famosab]

I would suggest to split this up into one PR by subtool / command :) regarding the md5sum instability I will add a comment

[famosab]

I added a few hints :)

[famosab]

We want the ext.args to be present in the main.nf.test file. That makes everything more readable in one go. See the module specifications for more info.

[famosab]

You can run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment

on this file to clean this up nicely.

[famosab]

Please remove this file :)

[famosab]

We want the ext.args to be present in the main.nf.test file. That makes everything more readable in one go. See the module specifications for more info.

[famosab]

I would just first assert the txt content of the filter output and then we can probably see why the md5sum is instable

Suggested change

	{ assert snapshot(process.out).match() }
	{ assert snapshot(
	path(process.out.filter[0][1]).readLines(),
	process.out.info,
	process.out.findAll { key, val -> key.startsWith("versions") },
	).match() }