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Update pydantic taxprofiler (#3872)
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### Changed

- Update Pydantic for Taxprofiler
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henrikstranneheim authored Oct 24, 2024
1 parent 2677669 commit 52f5f2e
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Showing 2 changed files with 6 additions and 2 deletions.
3 changes: 3 additions & 0 deletions cg/models/analysis.py
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Expand Up @@ -9,6 +9,9 @@
class AnalysisModel(BaseModel):
"""Metadata analysis model"""

class Config:
arbitrary_types_allowed = True


class NextflowAnalysis(AnalysisModel):
"""Nextflow's analysis results model."""
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5 changes: 3 additions & 2 deletions cg/models/taxprofiler/taxprofiler.py
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@@ -1,5 +1,6 @@
from pathlib import Path
from pydantic.v1 import BaseModel, Field

from pydantic import BaseModel, Field

from cg.constants.sequencing import SequencingPlatform
from cg.models.nf_analysis import NextflowSampleSheetEntry, WorkflowParameters
Expand Down Expand Up @@ -40,7 +41,7 @@ class TaxprofilerParameters(WorkflowParameters):
centrifuge_save_reads: bool = True
run_krona: bool = True
run_profile_standardisation: bool = True
clusterOptions: str = Field(..., alias="cluster_options")
clusterOptions: str = Field(alias="cluster_options")
priority: str


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