Store vcfs on a case level

[karlnyr]

The purpose of the code changes are as follows:

• Change the id to be case so that all of the vcfs are delivered to the case folder instead of in each sample folder.

Preparations:

How to prepare mutant for test:

• cd MUTANT
• bash mutant/standalone/deploy_hasta_update.sh stage <MUTANT_branch>

How to prepare cg for test:

• us
• Paxa and update cg:
  • paxa -u <user> -s hasta -r cg-stage
  • bash update-cg-stage.sh master
• If needed, paxa and update servers:
  • paxa -u <user> -s hasta -r servers-stage
  • bash update-servers-stage.sh <master/branch>

How to test:

Run in a tmux screen or similar if testing on a large dataset.

Test with cg:

• us
• cg workflow mutant start maturejay

Expected outcome:

• Produced files contain expected values

Review:

• Code reviewed by

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