🐛 Critical bug fix

[migbro]

Description

While investigating rMATS weirdness in Maris, it was discovered that read 2 (mates) was not passed properly to STAR after cutadapt if a user provided an adapter sequence. Changes overall include:

• Fixing that bug
• Making quality trimming optional
• Making variable read len for rMATs default per @naqvia recommendation
• Updates to docs

Fixes # https://github.com/d3b-center/bixu-tracker/issues/1856 and https://github.com/d3b-center/bixu-tracker/issues/1840

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)
• [ ] 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

• [ ] Cutadapt single qual
• [ ] Cutadapt diff qual
• [ ] Mates pass fix, see logs to confirm mates from cutadapt passed to STAR properly

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