feat: Deliver MultiQC intermediate files

[ivadym]

Description

Add MultiQC intermediates files to the deliverables .hk file.

Added

• MultiQC intermediate files to deliverables

Changed

• delivery.py, removing unused arguments

Documentation

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

Tests

Feature Tests

• N/A
• Test generation of the .hk file
  
• Test MultiQC files included in the deliverables .hk file with unique tags
  
• Test that different workflow generate the intermediate MultiQC expected files

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: Store intermediate MultiQC files for Balsamic hermes#95
• 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]

Integration Tests

• N/A
• Test MultiQC intermediate files stored in HK
  • Tested in Store intermediate MultiQC files for Balsamic hermes#95

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

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (790ad8a) 99.42% compared to head (fe40771) 99.44%.
Report is 88 commits behind head on develop.

Files	Patch %	Lines
BALSAMIC/models/validators.py	85.71%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1388      +/-   ##
===========================================
+ Coverage    99.42%   99.44%   +0.01%     
===========================================
  Files           41       40       -1     
  Lines         1916     1983      +67     
===========================================
+ Hits          1905     1972      +67     
  Misses          11       11              

Flag	Coverage Δ
unittests	99.44% <99.74%> (+0.01%)	⬆️

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[mathiasbio]

This looks great 🌟 Looks like you also took the opportunity to do some refactoring. Feels like this deliver.py is easier to read now! I just added a question, but even if you haven't tested it explicitly I trust in the logic of your code. Just wanted to make sure that it has been considered : )

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues

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

See analysis details on SonarCloud