Update use_read_count_threshold for taxprofiler

[sofstam]

Description

Changed

• According to previous communication, cust053 would like to have data and analysis even though they are just below the targeted threshold of 75%. In case the data are below the targeted threshold, they will assess if the quality of the data is good enough for the purposes. In this PR, the function use_read_count_threshold is updated to fit this purpose.

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 read_count_threshold -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 ...

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[ivadym]

I'm not sure this method is used somewhere, seems like it's just defined in the nextflow analysis api but it's never called 🤔

[fevac]

the parent method was removed there https://github.com/Clinical-Genomics/cg/pull/2886/files
so it has to be adapted on the nf-analysis class or has already be done and can just be removed

[sofstam]

I can remove those methods and test start-available for all pipelines (rare disease, tomte, taxprofiler, rnafusion)

[fevac]

not the test. Only the methods. I'm not sure if the behaviour is correct right now. Can you check?

[sofstam]

cg/cg/services/quality_controller/quality_checks/checks.py

Lines 25 to 53 in b6ad74c

	def get_sequencing_quality_check_for_case(case: Case) -> Callable:
	"""Return the appropriate sequencing quality checks for the workflow for a case."""
	workflow: Workflow = case.data_analysis
	case_passes_workflows = [
	Workflow.BALSAMIC,
	Workflow.BALSAMIC_PON,
	Workflow.BALSAMIC_QC,
	Workflow.BALSAMIC_UMI,
	Workflow.MIP_DNA,
	Workflow.MIP_RNA,
	Workflow.RAREDISEASE,
	Workflow.RNAFUSION,
	Workflow.TOMTE,
	]
	any_sample_in_case_has_reads_workflows = [
	Workflow.FLUFFY,
	Workflow.FASTQ,
	Workflow.MICROSALT,
	Workflow.MUTANT,
	Workflow.TAXPROFILER,
	]
	if workflow in case_passes_workflows:
	return SequencingQCCheck.CASE_PASSES
	elif workflow in any_sample_in_case_has_reads_workflows:
	return SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS
	raise ValueError(f"Workflow {workflow} does not have a sequencing quality check.")

It is correct, can test as well.