🐎 sentieon wf

[dmiller15]

Description

Creates a new alignment workflow using Sentieon's suite of tools. Small updates to existing tools. Still might need some cleanup.

Closes https://github.com/d3b-center/bixu-tracker/issues/1404 Part of https://github.com/d3b-center/bixu-tracker/issues/1405

Type of change

• [x] New feature (non-breaking change which adds functionality)
• [x] This change requires a documentation update

How Has This Been Tested?

• [x] https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/75e3ebf6-ad5d-4871-9f80-066bfee384d7/
• [x] https://github.com/d3b-center/bixu-tracker/issues/1405

Test Configuration:

• Environment: cwltool and cavatica
• Test files: see cavatica test; also this ticket https://github.com/d3b-center/bixu-tracker/issues/1405

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

[dmiller15]

@migbro Yes there are the warnings about secondaryFile misalignment but ultimately those don't affect the running as you can see here: https://cavatica.sbgenomics.com/u/d3b-bixu/ha-bam-benchmarking/tasks/5c533287-cf85-4357-82f9-42e0a64bf523/. gVCF creation goes off without a hitch. Ultimately I think it's just that the gVCF workflow is a bit out of date and doesn't have the appropriate declarations. Since this PR explicitly avoids delving into the gVCF workflow I'd rather leave those warning resolutions for a different time.