RNAFUSION: use config files instead of nf-core hasta profile

[rannick]

Description

Added

Changed

• Unified the config and param file generation for rnafusion with the other nf workflows, using https://github.com/Clinical-Genomics/servers/pull/1467

Fixed

How to prepare for test

• Ssh to relevant server (depending on type of change)
• 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_cg -t cg -b [THIS-BRANCH-NAME] -a

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

• 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 on ...
• Inform to ...

[rannick]

Tested with a case on stage, after review, one more test on prod should be done

[diitaz93]

Looks good 🚀

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[rannick]

Log deploy... done.
cg, version 64.4.24
remote: Enumerating objects: 34, done.
remote: Counting objects: 100% (34/34), done.
remote: Compressing objects: 100% (17/17), done.
remote: Total 34 (delta 17), reused 26 (delta 15), pack-reused 0 (from 0)
Unpacking objects: 100% (34/34), done.
From https://github.com/Clinical-Genomics/cg
   b70a21e..087fa6c  master     -> origin/master
 * [new branch]      make-sfffetching-apptag-base -> origin/make-sfffetching-apptag-base
 * [new tag]         v64.4.24   -> v64.4.24
From https://github.com/Clinical-Genomics/cg
 * [new tag]         v64.4.23   -> v64.4.23
Already on 'master'
Your branch is behind 'origin/master' by 4 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)
Updating b70a21e..087fa6c
Fast-forward
 .bumpversion.cfg                 |  2 +-
 cg/__init__.py                   |  2 +-
 cg/meta/workflow/rnafusion.py    | 11 ++++-------
 cg/models/cg_config.py           |  3 +++
 cg/models/rnafusion/rnafusion.py | 11 -----------
 cg/store/crud/read.py            |  2 +-
 pyproject.toml                   |  2 +-
 tests/conftest.py                | 10 +++++-----
 8 files changed, 16 insertions(+), 27 deletions(-)
/home/hiseq.clinical
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.