Notebook modules

[grst]

Attempt to implement generic modules for rendering Rmarkdown or jupyter notebooks into HTML reports.
I'm deviating from the one module - one PR rule here, because I feel the two should be discussed together.

The modules support

• Execute notebook and generate HTML report
• Jupyter notebooks can be in arbitrary jupytext formats
• Set sensible defaults for parallel computing (BLAS, MKL, numba etc.)
• Pass input files (e.g. data tables) to notebooks in a separate channel
• Retrieve output files ("artifacts") as an output channel
• Optionally, parametrize notebooks via a separate input channel.

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.
• Emit the <SOFTWARE>.version.txt 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:
  • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd
  • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
  • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd

[grst]

I added a few open questions as a code review - would be great if I could get some feedback!

[grst]

Asking additional review from @jianhong, who showed interest in such a module on slack.

[grst]

I added tests now, see the sister PR nf-core/test-datasets#297 in test-datasets.

[jfy133]

Mostly formatting, one suggestion and one possible suggestion to remove debugging stuff if it's ready.

[drpatelh]

Looks great @grst ! Mostly minor comments. Feel free to merge when they have been addressed!