✨ added xy ratio calculation tool

[dmiller15]

Description

This PR adds XY ratio stat calculation to the alignment workflow.

Closes https://github.com/d3b-center/bixu-tracker/issues/932

Type of change

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

How Has This Been Tested?

• [x] Tool and workflow passes cwltool validation
• [x] Test of tool with run turned off: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/bd83b354-9b2f-4e4d-ae8c-8e9f3596b039/
• [x] Test of tool with run turned on: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/42781d21-d65f-46ed-975f-b873be69f181/#
• [x] Test of new alignment workflow: https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/ebf74a14-08e1-49d1-b467-3b223b4544fc/#

Test Configuration:

• Environment: cwltool 3.0.20200807132242, 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

[yuankunzhu]

cc @zhangb1 for this PR as well. although this is still under reviewing, but we are planning to have {task_id}.ratio.txt as one of the alignment workflow output, so you can use that to predict gender

[dmiller15]

@yuankunzhu @migbro Took the suggestion to add a kill switch for the idxstats step. Testing of the individual tool looks good and the full workflow should be done sometime shortly. Please review.