🎉 add rmats

[dmiller15]

Description

This PR does four things:

1. Updates RNAseq workflow for sbpack (all I did was quote the sbg keys)
2. Ports rmats tools and workflows from https://github.com/d3b-center/pbta-splicing
3. Integrates the rmats workflow into the RNAseq pipeline
4. Changed the star align cwl so that it can handle uncompressed fastqs. The current pipeline fails during RSEM if the user provides uncompressed fastq files because our implementation of star align is specifically tailored to compressed files and returns an empty BAM if given uncompressed fastqs. So I just made it so if star align does not see the GZ file extension it does use zcat inappropriately.

Part of https://github.com/d3b-center/bixu-tracker/issues/1295

Type of change

Please delete options that are not relevant.

• [x] Bug fix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [x] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [x] This change requires a documentation update

How Has This Been Tested?

• [x] SE: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/5e5a062a-45ec-4be8-bef3-678f70ffadf8
• [x] PE: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/ebc1bb4e-4047-4e83-bfb9-8759ebcca608

Test Configuration:

• Environment:
• Test files:

Checklist:

• [x] My code follows the style guidelines of this project
• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I have added tests that prove my fix is effective or that my feature works
• [x] New and existing unit tests pass locally with my changes
• [x] Any dependent changes have been merged and published in downstream modules
• [x] I have checked my code and corrected any misspellings
• [x] I have committed any related changes to the PR

[dmiller15]

Ok I added the rmats inputs to the common inputs section and added a line about providing the rmats read length value.