feat: add msisensorpro container

[khurrammaqbool]

Description

Add MSIsensor-pro container

Added

• Add MSIsensor-pro container

Documentation

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

Tests

Feature Tests

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

Pipeline Integrity Tests

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

Clinical Genomics Stockholm

Documentation

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

User Changes

• 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
  • N/A
  • Updated: [Link]
• CG (CLI and delivered/uploaded files)
  • N/A
  • Updated: [Link]
• Servers (configuration files on Hasta)
  • N/A
  • Updated: [Link]
• Scout interface
  • 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.
  • 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
  • Code implements the intended features or fixes the reported issue.
  • Code follows the project's coding standards and style guide.
• Documentation
  • 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.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.48%. Comparing base (828cf3a) to head (7d529e6).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1444   +/-   ##
========================================
  Coverage    99.48%   99.48%           
========================================
  Files           40       40           
  Lines         1930     1932    +2     
========================================
+ Hits          1920     1922    +2     
  Misses          10       10           

Flag	Coverage Δ
unittests	99.48% <100.00%> (+<0.01%)	⬆️

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[mathiasbio]

Sounds good! Happy testing! 🌟 Going to be great to have this!

[ivadym]

Looks good! 💯

For next time, could you please provide a brief explanation if you choose not to address the review comments? Thanks!

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[khurrammaqbool]

Looks good! 💯

For next time, could you please provide a brief explanation if you choose not to address the review comments? Thanks!

Which comment did I not address? I may have missed something. I mean other than -y.

[ivadym]

Looks good! 💯
For next time, could you please provide a brief explanation if you choose not to address the review comments? Thanks!

Which comment did I not address? I may have missed something. I mean other than -y.

I unresolved the other one, it was just about the chsh command, I'm not sure to which user we'll change the shell if we don't provide it as an argument 🤔