feat(pipeline): Refactor to workflow

[henrikstranneheim]

Description

Changed

• Refactor pipeline to workflow in CGDeliverables

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 refactor-pipeline-to-workflow-cgdeliverabels

How to test

• [ ] Do ...

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

• [x] 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: 2 lines in your changes are missing coverage. Please review.

Comparison is base (fa43a69) 90.16% compared to head (b85d1b3) 90.17%. Report is 4 commits behind head on main.

Files	Patch %	Lines
cg_hermes/cli/export.py	50.00%	1 Missing :warning:
cg_hermes/cli/validate.py	66.66%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #93 +/- ## ========================================== + Coverage 90.16% 90.17% +0.01% ========================================== Files 25 25 Lines 559 560 +1 ========================================== + Hits 504 505 +1 Misses 55 55 ``` | [Flag](https://app.codecov.io/gh/Clinical-Genomics/hermes/pull/93/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/93/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Clinical-Genomics) | `90.17% <87.50%> (+0.01%)` | :arrow_up: | 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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[henrikstranneheim]

Nice, I guess we'll update the CLI later 💯

Yes, more PRs will follow.

[henrikstranneheim]

Deployed to production:

Log deploy... done.
hermes version: 3.0.0