feat: addition of vembrane sort module

[mkatsanto]

PR checklist

Fixes #9265

Addition of the vembrane sort module https://github.com/vembrane/vembrane

• 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
• 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]

Suggested change

	{ assert snapshot(process.out).match() }
	{ assert snapshot(
	process.out,
	path(process.out.versions[0]).yaml
	).match() }

[famosab]

This is added in the other PR right?, can you remove it here? :)

[famosab]

Sorry, what I meant: can you please do one PR per module :) meaning one seperate one for vembrane/table?

[famosab]

Can you run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment modules/nf-core/vembrane/sort/main.nf

please? :)

[famosab]

vembrane sort: error: argument --output-fmt/-O: invalid choice: 'vcf.gz' (choose from vcf, bcf, uncompressed-bcf)

[famosab]

Seems like gzipped vcfs are not allowed. I would suggest to open an issue over at the vembrane repo to request that and remove it from the module for now :) You can link to the PR in the issue you open :)

[famosab]

Suggested change

	test("homo_sapiens - [vcf] - vcf - compressed_output") {
	config "./nextflow.config"
	when {
	params {
	vembrane_args = '--output-fmt vcf.gz'
	}
	process {
	"""
	input[0] = [
	[ id:'test_gz' ], // meta map
	file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
	]
	input[1] = 'QUAL'
	"""
	}
	}
	then {
	assertAll(
	{ assert process.success },
	{ assert snapshot(process.out).match() }
	)
	}
	}

[famosab]

Suggested change

	pattern: "*.{vcf,vcf.gz}"
	pattern: "*.{vcf,bcf}"