Changes for running NIPT on NovaSeqX

[islean]

Description

This PR collects the changes needed for running NIPT on NovaSeqX. Needs to be merged together with changes in servers and in statina

Servers PR: https://github.com/Clinical-Genomics/servers/pull/1844
Statina PR: Clinical-Genomics/statina#250

Added

• Data set parameter parsed from the statina section of CGConfig. Used when uploading to statina.

Changed

• Removed the external ref flag from Fluffy start and run
• Added batch ref flag to Fluffy start and run

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 integration-branch-nipt-novaseqx -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 ...

[RasmusBurge-CG]

Setting default data set, tested and successful see https://github.com/Clinical-Genomics/servers/issues/1843

[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

[RasmusBurge-CG]

Great! 👍

[RasmusBurge-CG]

##Deployment

Stage

/home/hiseq.clinical
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/hiseq.clinical
done.
Log deploy... done.
cg, version 85.6.0
[10:02] [hiseq.clinical@hasta:~] [S_base]  $

Prod

Fast-forward
 .bumpversion.cfg                               |  2 +-
 cg/__init__.py                                 |  2 +-
 cg/cli/workflow/fluffy/base.py                 | 21 +++++++--------------
 cg/meta/upload/nipt/models.py                  |  1 +
 cg/meta/upload/nipt/nipt.py                    |  2 ++
 cg/meta/workflow/fluffy.py                     |  7 ++-----
 cg/models/cg_config.py                         |  7 ++++---
 pyproject.toml                                 |  2 +-
 tests/conftest.py                              |  1 +
 tests/meta/upload/nipt/test_models.py          |  3 ++-
 tests/meta/upload/nipt/test_nipt_upload_api.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 tests/meta/workflow/test_fluffy.py             | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 vulture_whitelist.txt                          |  5 +++--
 13 files changed, 165 insertions(+), 28 deletions(-)
 create mode 100644 tests/meta/workflow/test_fluffy.py
/home/hiseq.clinical
INFO  [alembic.runtime.migration] Context impl MySQLImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
[10:16] [hiseq.clinical@hasta:~] [P_base]  $