🚲 hc wf and alignemnt use same subwf

[dmiller15]

Description

Changes:

• BAM to gVCF subworkflow tools updated to what is run in the CRAM to gVCF standalone
• Alignment input to generate_gvcf step updated to fulfill new requirements
• CRAM to gVCF now uses same generate_gvcf subworkflow as alignment
• Iterate release
• Cleaned up some trailing whitespaces

Closes https://github.com/d3b-center/bixu-tracker/issues/822

Type of change

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

How Has This Been Tested?

• [x] Old prod alignment: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/e4b6abd5-84d4-4f94-a13c-e2fbf4b27ccb/
• [x] New prod alignment: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/a955ae0d-bf9a-4144-a4b5-edd3d1d89abc/
• [x] Old cram to gvcf: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/75c1de20-1eeb-4f57-9c28-1f307a361ef0/
• [x] New cram to gvcf: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/7e33b701-3c76-4695-944e-4350c847b9e2/
• [x] Both pass cwltool validation

Checking the gvcf stats, old & new have identical stats indicating that nothing has been broken in the update.

Test Configuration:

• Environment: cwltool 3.0.20200807132242, 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