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Add new process udf for NA24385 prep control to arnold #500

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May 6, 2024
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4 changes: 3 additions & 1 deletion cg_lims/EPPs/files/sample_sheet/create_sample_sheet.py
Original file line number Diff line number Diff line change
Expand Up @@ -152,7 +152,9 @@ def calculate_index_hamming_distance(
return string_hamming_distance(
index_1=index_1.sequence[-len(index_2.sequence) :], index_2=index_2.sequence
)
message: str = f"Non-supported index type identified for indexes {index_1.sequence} and {index_2.sequence}: '{index_1.type}'."
message: str = (
f"Non-supported index type identified for indexes {index_1.sequence} and {index_2.sequence}: '{index_1.type}'."
)
LOG.error(message)
raise InvalidValueError(message)

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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

class ProcessUDFs(BaseModel):
performance_NA24143: Optional[str] = Field(None, alias="Batch no Prep Performance NA24143")
performance_NA24385: Optional[str] = Field(None, alias="Batch no Prep Performance NA24385")
GMCKsolid_HD827: Optional[str] = Field(None, alias="Batch no GMCKsolid-HD827")
GMSlymphoid_HD829: Optional[str] = Field(None, alias="Batch no GMSlymphoid-HD829")
GMSmyeloid_HD829: Optional[str] = Field(None, alias="Batch no GMSmyeloid-HD829")
Expand Down
3 changes: 1 addition & 2 deletions cg_lims/options.py
Original file line number Diff line number Diff line change
Expand Up @@ -394,7 +394,7 @@ def concentration_threshold(help: str = "Threshold for concentrations.") -> clic
def size_bp(help: str = "Fragment size in base pairs.") -> click.option:
return click.option("--size-bp", required=True, help=help)


def root_path(
help: str = "Root path to be used by the script to find files.",
) -> click.option:
Expand Down Expand Up @@ -445,4 +445,3 @@ def well_udf(help: str = "UDF name for artifact well.") -> click.option:

def container_name_udf(help: str = "UDF name for container name.") -> click.option:
return click.option("--container-name-udf", required=False, default=None, help=help)

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