🦅 Release/mb 4.00 release prep

[migbro]

Description

These updates are to be the finishing touches before release. I have done the following:

• Removed deprecated tools and workflows. Since they are not relevant to this workflow, but also exist in the releases in which they were, I think this helps clean things up nicely
• Changed default inputs to match arriba heavy params. Please double check against STAR doc https://github.com/kids-first/kf-rnaseq-workflow/blob/release/mb-4.00-release-prep/docs/STAR_2.7.10a.md to ensure I have achieved this.
• Added a bam-to-cram step. I think, unless one can think of a reason that conversion back to bam would fail, that we can store the genomic bams as cram, saving us space and money. Transcript bams will remain as such.
• Updated awk filtering step to not use sample name to fit prod file name output

Fixes # https://github.com/d3b-center/bixu-tracker/issues/1399

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)
• [ ] 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

• [x] Shakedown run in progress here: https://cavatica.sbgenomics.com/u/kids-first-drc/kids-first-drc-rnaseq-workflow/tasks/e8a1b6de-c40d-4e9d-8f04-f476f04f39eb/
• [ ] Test B

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
• [ ] I have committed any related changes to the PR

[migbro]

I will likely not quite merge this request even if it passes review until I meed with Ops

[sickler-alex]

We mentioned in code review maybe creating another step in the workflow that has an input either "arriba-heavy" or "GTEX" and sets all of the parameters. The tool should also take all of the other parameters as optional inputs in case a user wanted to manually change them. Or allow a hybrid, say if they wanted to run most of the GTEX values but change a handful.