🚸 Optional inputs for Cavatica Batch Tasks

Description

Updates the RNAseq workflow to be more Cavatica Batch submission friendly. No longer require values that would need to be unique in a batch submission (output_basename, sample_name, and outSAMattrRGline). Those values are now, if not provided, based on the reads1 file basename through the use of a quick expressiontool.

Updates the documentation slightly to reflect the new optional values and how we process that. Also cleaned up some formatting and iterated release number.

Closes https://github.com/d3b-center/bixu-tracker/issues/1508

Type of change

[x] New feature (non-breaking change which adds functionality)

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] Do not provide optional values: https://cavatica.sbgenomics.com/u/kids-first-drc/kids-first-drc-rnaseq-workflow/tasks/cfd52df7-2c22-4f05-ae45-35326b2c1835/
[x] Provide optional values: https://cavatica.sbgenomics.com/u/kids-first-drc/kids-first-drc-rnaseq-workflow/tasks/9df7de2a-138e-4f0c-ab7a-4e75792736ab/

Test Configuration:

Environment: cwltool, cavatica
Test files: see cavatica tests

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

kids-first / kf-rnaseq-workflow