feat: Remove GATK3

[khurrammaqbool]

Description

Remove GATK3 from the workflow [PR description]

Removed

• GATK3 from the workflow and from the container

Documentation

• [x] N/A
• [ ] Updated Balsamic documentation to reflect the changes as needed for this PR.
  • [Document Name]

Tests

Feature Tests

• [x] N/A
• [ ] Test [Description]
  • [Screenshot]

Pipeline Integrity Tests

• Report deliver (generation of the .hk file)
  • [x] N/A
  • [ ] Verified
• TGA T/O Workflow
  • [x] N/A
  • [ ] Verified
• TGA T/N Workflow
  • [x] N/A
  • [ ] Verified
• UMI T/O Workflow
  • [x] N/A
  • [ ] Verified
• UMI T/N Workflow
  • [x] N/A
  • [ ] Verified
• WGS T/O Workflow
  • [x] N/A
  • [ ] Verified
• WGS T/N Workflow
  • [x] N/A
  • [ ] Verified
• QC Workflow
  • [x] N/A
  • [ ] Verified
• PON Workflow
  • [x] N/A
  • [ ] Verified

Clinical Genomics Stockholm

Documentation

• Atlas documentation
  • [x] N/A
  • [ ] Updated: [Link]
• Web portal for Clinical Genomics
  • [x] N/A
  • [ ] Updated: [Link]

User Changes

• [x] N/A
• [ ] This PR affects the output files or results.
  • [ ] User feedback is considered unnecessary because [Justification].
  • [ ] Affected users have been included in the development process and given a chance to provide feedback.

Infrastructure Changes

• Stored files in Housekeeper
  • [x] N/A
  • [ ] Updated: [Link]
• CG (CLI and delivered/uploaded files)
  • [x] N/A
  • [ ] Updated: [Link]
• Servers (configuration files on Hasta)
  • [x] N/A
  • [ ] Updated: [Link]
• Scout interface
  • [x] N/A
  • [ ] Updated: [Link]

Checklist

[!IMPORTANT]
Ensure that all checkboxes below are ticked before merging.

For Developers

• PR Description
  • [ ] Provided a comprehensive description of the PR.
  • [x] Linked relevant user stories or issues to the PR.
• Documentation
  • [ ] Verified and updated documentation if necessary.
• Tests
  • [ ] Described and tested the functionality addressed in the PR.
  • [ ] Ensured integration of the new code with existing workflows.
  • [ ] Confirmed that meaningful unit tests were added for the changes introduced.
  • [ ] Checked that the PR has successfully passed all relevant code smells and coverage checks.
• Review
  • [ ] Addressed and resolved all the feedback provided during the code review process.
  • [ ] Obtained final approval from designated reviewers.

For Reviewers

• Code
  • [x] Code implements the intended features or fixes the reported issue.
  • [x] Code follows the project's coding standards and style guide.
• Documentation
  • [x] Pipeline changes are well-documented in the CHANGELOG and relevant documentation.
• Tests
  • [ ] The author provided a description of their manual testing, including consideration of edge cases and boundary conditions where applicable, with satisfactory results.
• Review
  • [ ] Confirmed that the developer has addressed all the comments during the code review.