Force storage of incomplete analyses

[ivadym]

Description

This PR will allow us to force the generation of the HK bundle of failed analyses. It addresses some of the points from https://github.com/Clinical-Genomics/cg/issues/2702.

How to prepare for test

• [ ] ssh to hasta.scilifelab.se
• [ ] Use stage: us
• [ ] Paxa the environment: paxa
• [ ] Install on stage (example for hasta): bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_hermes -t hermes -b [THIS-BRANCH-NAME]

How to test

• /hermes validate deliverables --workflow <workflow>
• /hermes convert deliverables --workflow <workflow>
• Tested as part of https://github.com/Clinical-Genomics/cg/pull/3340

Expected test outcome

• [ ] Check that ...
• [ ] Take a screenshot and attach or copy/paste the output.

Review

• [ ] Tests executed by
• [ ] "Merge and deploy" approved by Thanks for filling in who performed the code review and the test!

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

Implementation Plan

• [ ] Document in ...
• [ ] Deploy this branch
• [ ] Inform to ...

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 53.33333% with 14 lines in your changes missing coverage. Please review.

Project coverage is 92.61%. Comparing base (afef44b) to head (4019f30). Report is 1 commits behind head on main.

Files	Patch %	Lines
cg_hermes/cli/common.py	25.00%	6 Missing :warning:
cg_hermes/cli/validate.py	44.44%	5 Missing :warning:
cg_hermes/deliverables.py	60.00%	2 Missing :warning:
cg_hermes/cli/convert.py	87.50%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #113 +/- ## ========================================== - Coverage 93.01% 92.61% -0.40% ========================================== Files 26 26 Lines 916 921 +5 ========================================== + Hits 852 853 +1 - Misses 64 68 +4 ``` | [Flag](https://app.codecov.io/gh/Clinical-Genomics/hermes/pull/113/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/Clinical-Genomics/hermes/pull/113/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | `92.61% <53.33%> (-0.40%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics#carryforward-flags-in-the-pull-request-comment) to find out more.

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[ivadym]