Rmats prep PR

[akaviaLab]

PR checklist

This is a PR of rmats/prep.
RMATS processes BAM files from RNAseq and identifies splice junctions used, and differences between groups of samples.
RMATS is composed of 4 stages (that can be run together), but I'm planning to split into steps

1. Prep which processes BAM files (this PR)
2. Post, which process the output of prep
3. Dividing the post files into groups, based on the statistics
4. Stats - comparing two groups. Since stats can only compare two groups, I will set up stage 3 to read contrasts and set up the groups.

I will then set up a workflow that does all 4.

Eventually, the workflow will close #8699 . Please do not close the issue yet.

This creates the main.nf for rmats.py prep command, and adds tests for multiple parameters that can be given to rmats prep.

• 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
• 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

[akaviaLab]

Let me knwo what you think about these comments

[SPPearce]

@akaviaLab , do you need a re-review on this?

[akaviaLab]

I need an approval from a core maintainer to merge. I'll fix the URL, but apart from tgat, can you approve? Ive changed everything as discussed.

…

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[akaviaLab]

@akaviaLab , do you need a re-review on this?

Yes please! I've fixed everything, but I need you to approve before merging.

[akaviaLab]

Thank you!