Update raredisease with saltshaker, combined nuc+mito SVs

[ieduba]

Description

Update raredisease delivery to replace eklipse output with saltshaker output. Also combined nuclear and mitochondrial SV calling.

Added

Changed

• Removed call_sv_mt vcf output, since now all SV vcfs are combined.
• Also updated the path for all call_sv to reflect the combined calling.
• Changed ekplise output to saltshaker output (and removed the extra eklipse output for which there is no equivalent in saltshaker)

Fixed

Testing

How to prepare for test

• ssh to Hasta
• Test your branch with

hermes-test-deploy <branch-name>
hermes-test <command here>

How to test

• login to ...
• do ...

Expected test result

• check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• code approved by
• tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions