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Update use_read_count_threshold for taxprofiler #3196

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Update use_read_count_threshold for taxprofiler #3196

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Update use_read_count_threshold for taxprofiler
sofstam May 2, 2024
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sofstam May 2, 2024
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sofstam May 2, 2024
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sofstam May 2, 2024
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6 changes: 6 additions & 0 deletions cg/meta/workflow/taxprofiler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,3 +104,9 @@ def get_multiqc_search_patterns(self, case_id: str) -> dict:
def get_genome_build(self, case_id: str) -> str:
"""Return the reference genome build version of a Taxprofiler analysis."""
return GenomeVersion.T2T_CHM13.value

@property
def use_read_count_threshold(self) -> bool:
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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 🤔

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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

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

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

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@sofstam sofstam May 3, 2024 •
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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.

"""Defines whether the threshold for adequate read count should be passed for all samples
when determining if the analysis for a case should be automatically started."""
return False
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