Update SVDB to 2.8.2

[alkc]

Description and reviewer info

Adds:

• SVDB container

Updates:

• SVDB from 2.2.0 to 2.8.2

Changes:

• (Probably) Restructure SVDB processes a bit
• Input VCFs are sorted on filename prior to being merged, which should fix:
  Order of VCFs to SVDB merge not consistent between subsequent reruns of same sample #216
• Moves out most of remaining container pathspecs to config
• cnvkit container frozen from twist_myeloid_active.sif to twist_myeloid_2020-06-17.sif

Closes #118, fixes #244, fixes #216

TODO:

• Put post-processing perl script calls in separate process
  • svdb_merge
  • svdb_merge panel
• Complete onco run w/ svdb 2.8.2
• Complete wgs run w/ svdb 2.8.2
• Set up test plan
  • Diff a few SV VCFs and see what diffs
  • How major of a validation do we need to do?
• (Bonus) move remaining container specs into config

Type of change

• Documentation
• Patch
• Minor change
• Major change

Checklist

• Self-review of my code
• Update the CHANGELOG
• Tag the latest commit (vX.Y.Z format)
• Log samples used for testing in the Verification_samples_log Excel sheet

Documentation

• At least one other person has reviewed my changes (not required for trivial changes)

Patch

• Stub run completes without errors or new warnings
• At least one other person has reviewed and approved my code (not required for trivial changes)

Major / Minor change

• Stub run completes without errors or new warnings
• onco run finishes without any new warnings/errors and the results can
  be loaded into scout
• wgs single run finishes without any new warnings/errors and the results
  can be loaded into scout
• wgs trio run finishes without any new warnings/errors and the results
  can be loaded into scout
• At least one other person has reviewed and approved my code
• I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

• Alexander
• Jakob
• Paul
• Ryan
• Viktor

(Add if missing)

Testing performed by

• Alexander
• Jakob
• Paul
• Ryan
• Viktor

[alkc]

Using an SVDB container from galaxy proj. those do not seem to have perl installed. the follow up merge_callset perl script calls need to be moved to own process, or - if no other special dependencies - converted to python.