Add Cellsnp to modules

[wxicu]

PR checklist

Related to #5072
Add cellsnp-lite.

• 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

[tstoeriko]

Good job so far! I've made some suggestions, but I'm still new to nf-core, so it's probably a good idea to have someone else look at the module, too.

[wxicu]

@tstoeriko thanks for your detailed suggestion! I have now splitted cellsnp into two submodules for mode a and b (also according to the documentation[https://cellsnp-lite.readthedocs.io/en/latest/main/manual.html]) to control the input type. Both Mode 1a and mode 2a requie only a single bam file. hope this will make the structure more clear.
I have also tried to make the output files included in the snapshot as many as possible

[SPPearce]

This looks very nice.
I have a question though, the docs talk about 4 modes, calling them Mode1a, Mode1b, Mode2a, Mode2b. Which is this? Should it be e.g. mode1a rather than modea?

[SPPearce]

This looks very nice. I have a question though, the docs talk about 4 modes, calling them Mode1a, Mode1b, Mode2a, Mode2b. Which is this? Should it be e.g. mode1a rather than modea?

Oh, I see that you have indeed answered this in the comment above, so this is appropriate for either mode1a or mode2a.
Just a few minor things then it is ready to go.

[SPPearce]

Suggested change

	file(params.modules_testdata_base_path + /genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf', checkIfExists: true),
	file(params.modules_testdata_base_path + '/genomics/homo_sapiens/demultiplexing/donor_genotype_chr21.vcf', checkIfExists: true),

[wxicu]

thank you for pointing out. I have just found the error LOL

[wxicu]

@SPPearce I tried your suggestion but didnt pass the tests due to the error Not a valid path value type: groovyx.gpars.dataflow.DataflowVariable (DataflowVariable(value=null)) . It seems like I was trying to add a channel to the input channel. So i go back to the previous version now