Adding MIP validation cases to fastq.py

[henningonsbring]

This PR adds cases that should not be compressed since these families are often used for validation.

How to prepare for test

• wait for the automatic fastq compression to start

Expected test outcome

• Check that the problematic/validation cases where skipped
• Take a screenshot and attach or copy/paste the output.

Review

• code approved by @moonso
• tests executed by
• "Merge and deploy" approved by @moonso
  Thanks for filling in who performed the code review and the test!

This version is a

• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[coveralls]

Coverage increased (+0.003%) to 71.519% when pulling 939b0e4 on henningonsbring-patch-1 into 30775ea on master.

[Mropat]

Could we also put keenviper (mip-dna) and sharpparrot (mip-rna) in the cases to ignore list?

Maybe make their own list of validation samples, and unpack both validation list and problematic cases list when skipping

[moonso]

Nice ⭐

[Mropat]

Are we sure the only way to test this is to deploy? There was no test for skipping cases in compress?

[Mropat]

You can create tests for this by:

in tests/cli/compress/ you could do either:
1.

• Add problematic families to populated compress store in tests/cli/compress/conftest.py
• Write test for fastq_cmd checking the log for skipped case message

• Write test for fastq_cmd while adding the problematic cases to ready-made populated_compress_store, checking the log for skipped case message

[hassanfa]

Could we add the following to the list as well?

moralgoat - wgs paired
fleetjay - wgs single
bosssponge - panel single
unitedbeagle - panel paired

I test run on these when testing BALSAMIC releases.

Thanks!

[Mropat]

It would be great to add a test for this, but since this might be not the n1 prio right now, we could deploy this as is

[moonso]

@henningonsbring is this ready?

[henningonsbring]

No, there is something I need to solve in production before I deal with this

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities (and 0 Security Hotspots to review)
0 Code Smells

No Coverage information
0.0% Duplication

[Mropat]

Deployed hasta-stage

Deployed on hasta-prod

[Mropat]

Congratulations @henningonsbring on your first contribution to cg! 🥳

[moonso]

Nice work @henningonsbring !

[henningonsbring]

Thank you for the help! :)