Fix: Update Cellranger/multi to reinclude functionality from previous PR update

[mahesh-panchal]

Description

Related to #11066 . Adds back in functionality from the python template that was accidentally dropped.

• Adds options for all input types
• Explicitly tests for certain keys.

PR checklist

• 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

[mahesh-panchal]

@leandrotiburske @fmalmeida The PR is ready and I think I have the flags in, but please check. From today I won't be near a computer to make updates so I made this branch on nf-core modules where you can both push/pull your own changes onto this branch.

The tests on this module look like they really need updating as well, but that's perhaps outside the scope. I leave this up to you both now.

[mahesh-panchal]

This PR should remove the old python template too since it's redundant.

[fmalmeida]

Hi @leandrotiburske,

Do you think you can take over from here to do the final amendments?

As @mahesh-panchal mentioned, the try is to move all the logic into the module itself.

So, could you double check if all the functionality from before is now there so to remove the template script?

As Mahesh, I am also not fluent in this tool, I had only helped out on the code but someone else was assessing the results ... so I believe it would be really good if someone that knows how the results should be could take a closer look.

I am on holidays until next Wednesday and I only have a phone, so I cannot help with the code until there but I can help with comments and review.