💪 Upgrade gencode reference and add new SW Versions

[migbro]

Description

This is part of the effort to coordinate with GTeX and Broad to upgrade references and software versions used in our RNAseq pipelines. The following new tools have been added:

• STAR 2.7.10a
• STAR-Fusion 1.10.1
• Arriba 2.2.1 Documentation corresponding to each new tool has been made in the docs folder Other tools have been refactored to fit the existing RNAseq workflow and a near-future workflow:
• rsem v1.3.1
• samtools_sort
• arriba 1.1.0

Part of # (issue)

Type of change

Please delete options that are not relevant.

• [ ] 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)
• [ ] This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration All tools pass local cwltool validation +. Note, while a tool for creating a STAR fusion reference exists, I do not have a successful run. It theoreticaly should work with my latest changes but is slow and costly and one ought to do it interactively as task failures lead to several hours of life lost.

• [ ] STAR 2.7.10a
• [ ] STAR genome generate
• [ ] STAR-Fusion 1.10.1
• [ ] rsem v1.3.1
• [ ] rsem prepare reference
• [ ] Arriba v2.2.1 call
• [ ] Arriba v2.2.1 draw
• [ ] samtools sort
• [ ] "old" wf with refactored tools

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
• [ ] 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