New module: whatshap/phase

[HaidYi]

PR checklist

Closes #9427

• 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.
• 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
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[famosab]

Few minor things :)

[famosab]

Can you also add a snapshot please?

[HaidYi]

Yes, the snapshot is added now. Here, I don't add the vcf as it will output the local dir to the snapshot file.

[famosab]

Suggested change

	{ assert process.success }
	{ assert process.success }
	{ assert snapshot(process.out).match() }

This should work for the stub test :)

[famosab]

Can you run

nextflow lint ...

on this file? :)

[HaidYi]

Remove a warning.

[famosab]

Sorry let me be more specific :)

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

[HaidYi]

@famosab Could you clean up the additional ci/cd for this PR?