Add subtool cellranger aggregate

[alenaboos]

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 >Not possible: module uses a Python template; Nextflow eval() output is Bash-only. Same limitation as cellranger/count.
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• Use BioConda and BioContainers if possible to fulfil software requirements. > Not available for conda
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
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    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
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[alenaboos]

The conda tests are failing, but cellranger does not exist for conda. Therefore, I included an error message when running the module with the conda profile similar to the cellranger count module.

[SPPearce]

Is this just a python wrapper to run a command line tool? Because if so, you should just run directly in the main.nf without involving python.

[alenaboos]

Yes, I did it similar to the cellranger count module, but I will add the command to the main.nf. The command requires to have the input files as a csv table. Should this be another process in the actual pipeline or should I also add the csv generation to this module?

[SPPearce]

That depends on how complex the csv generation is, but if it is just a list then should be able to be done within this module

[alenaboos]

I included the csv file generation into the module and also added the command directly instead of providing it as a py script.