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fix Enum issue, and add BaseSpace Run name to script
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Karl-Svard committed Nov 15, 2023
1 parent 6c92f5f commit bd7efec
Showing 1 changed file with 14 additions and 4 deletions.
18 changes: 14 additions & 4 deletions cg_lims/EPPs/udf/set/set_sequencing_settings.py
Original file line number Diff line number Diff line change
Expand Up @@ -43,16 +43,26 @@ def get_flow_cell_type(process: Process) -> str:
return flow_cell_type


def get_flow_cell_name(process: Process) -> str:
"""Return the flow cell name of the step."""
containers = process.output_containers()
return containers[0].name


def set_process_udfs(process: Process, parent_process: Process) -> None:
"""Set Prepare for Sequencing (NovaSeq X) process UDFs."""
library_tube_strip: str = get_library_tube_strip(process=parent_process)
flow_cell_type: str = get_flow_cell_type(process=parent_process)
flow_cell_name: str = get_flow_cell_name(process=process)
read_length: int = DEFAULT_READ_LENGTHS[flow_cell_type].value
index_length: int = DEFAULT_INDEX_LENGTHS[flow_cell_type].value
process.udf["Library Tube Strip ID"] = library_tube_strip
process.udf["Run Mode"] = flow_cell_type
process.udf["Read 1 Cycles"] = DEFAULT_READ_LENGTHS[flow_cell_type]
process.udf["Read 2 Cycles"] = DEFAULT_READ_LENGTHS[flow_cell_type]
process.udf["Index Read 1"] = DEFAULT_INDEX_LENGTHS[flow_cell_type]
process.udf["Index Read 2"] = DEFAULT_INDEX_LENGTHS[flow_cell_type]
process.udf["Read 1 Cycles"] = read_length
process.udf["Read 2 Cycles"] = read_length
process.udf["Index Read 1"] = index_length
process.udf["Index Read 2"] = index_length
process.udf["BaseSpace Run Name"] = flow_cell_name
process.put()


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