feat (closes #7246): add new component: leafcutter/differentialsplicing

[JTL-lab]

PR Description

This PR adds a new module leafcutter/differentialsplicing for running Leafcutter differential splicing analysis to determine statistically significant junction usage changes between biological conditions of interest. This module relies on the new Python reimplementation of Leafcutter (leafcutter-ds) here (also documented in the meta.yml).

PR checklist

Closes #7246

• 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]

Try this:

Suggested change

	{ assert snapshot(
	process.out.findAll { key, val -> key.startsWith('versions') },
	process.out.cluster_significance.collect { file(it[1]).getName() },
	process.out.effect_sizes.collect { file(it[1]).getName() }
	).match() },
	// Check non-deterministic files exist
	{ assert file(process.out.cluster_significance[0][1]).exists() },
	{ assert file(process.out.effect_sizes[0][1]).exists() }
	{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}

[SPPearce]

Suggested change

	assertAll(
	{ assert process.success },
	{ assert snapshot(process.out).match() },
	{ assert process.out.cluster_significance != null },
	{ assert process.out.effect_sizes != null }
	)
	assert process.success
	assertAll(
	{ assert snapshot(sanitizeOutput(process.out)).match() }
	)

[SPPearce]

Shouldn't need num_threads in here, that should already be in the tool?

[SPPearce]

Is this required?

[SPPearce]

Is this an appropriate requirement, how much RAM does the tool generally take?

[SPPearce]

Suggested change

	// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.