⚾️ sample name renamed to basename

[dmiller15]

Description

The variable sample_name is being used in an outdated fashion as the basename for all outputs. This became apparent with the addition of annoFuse written in our current best practices. As such, this PR folds sample_name into the output_basename that came with annoFuse. AnnoFuse gets to keep sample_name to itself as its the only tool using it within the files.

Closes https://github.com/d3b-center/bixu-tracker/issues/839

Type of change

Please delete options that are not relevant.

• [x] Bug fix (non-breaking change which fixes an issue)

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] Cavatica: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/bacde8a0-a818-4e23-bcd3-291bfe6345fc/

Test Configuration:

• Environment: Cavatica
• Test files: See Cavatica test

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