Add velocyto from bam for cellranger

[agalitsyna]

This PR adds a velocyto option to Cellranger branch of the pipeline, see #525 for more discussion.
By default the parameter is disabled, and can be switched on by --run_velocyto true.

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! -- No tests are needed.
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• NA: If necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated. -- Not needed
• Output Documentation in docs/output.md is updated. -- Not needed b/c velocyto if an option
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors). -- Nothing to be done

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[fmalmeida]

Had one comment regarding parameter syntax.

Otherwise code looks sane. But, since it adds a new tool and new outputs, it would be good to have the documentation updated to showcase it

[fmalmeida]

I wonder if, to align more with the other parameters syntax, would make sense to change it to skip_velocyto=true.

Any options @nictru @grst?