Runtime Parameters

Overview

This section details the process of defining parameters in a workflow that can then be set by a user when starting a run.

Parameters are variable values in a workflow that a user does not want to ‘hardcode’ in the workflow definition but instead wants to define them when going through the process of starting a run on LINQ.

An example would be defining a boolean parameter that determines if a labware would undergo a specific task or not.

Defining Parameters

Parameters can only be used in task arguments.

Four different parameter types can be defined: Boolean, Float, Integer and String parameters. See each class definition below.

Tip

String parameters can also be used to parameterize file paths.

Here are some example parameter definitions:

from linq.parameters import (
    BooleanParameterDefinition,
    FloatParameterDefinition,
    StringParameterDefinition
)

cold_plate_temperature = FloatParameterDefinition(
 id="cold_plate_temperature",
 name="Cold Plate Temperature",
 default=10.0,
 )

centrifuge_option = BooleanParameterDefinition(
 id="scan_barcode",
 name="Scan Barcode",
 default=False
 )

method_file_path = StringParameterDefinition(
 id="method_file_path",
 name="Method File Path",
 is_file_path=True,
 )

For workflow tasks to access parameters, the parameter definitions need to be defined (in a list) as an argument in the workflow object

workflow = Workflow(
    ...
    parameter_definitions=[cold_plate_temperature, centrifuge_option, method_file_path]
)

These parameters can then be used in the inputs argument of a task by referencing the desired parameter id

incubate_in_cold_plate = workflow.add_task(
    ActionTask(
        ...
        inputs=Inputs(temperature=ParameterReference(parameter_id="cold_plate_temperature")),
    )
)

Setting Parameters

Parameters are set in the publish stage of workflow execution. Parameters can be set in two ways:

As a response to CLI prompts.
By providing a parameters.json configuration file.

Setting parameters through CLI prompts

When publishing a workflow with parameters defined and no parameters file provided, parameters are set through prompts on the command line.

foo@bar:~$ linq workcell publish <workflow-id>
Enter Float value for parameter 'Cold Plate Temperature' or hit enter to use default value '10.0':

Once all parameters are provided the publish command will execute.

Setting parameters through a parameters file

Alternatively, rather than manually entering every parameter value through prompts on the command line, a JSON file specifying parameter values can be provided as an argument to the publish command.

linq workcell publish <workflow-id> --parameters <path_to_parameters_json>

Example parameters JSON:

{
  "Cold Plate Temperature": 10.0,
  "Scan Barcode": true,
  "Method File Path": "path/to/method_file.txt"
}

Note

The parameters JSON schema is {<Type>ParameterDefinition.name: value}.

Parameter Types

class linq.parameters.BooleanParameterDefinition(*, id: str = ..., name: str = ..., always_required: bool = False, default: bool | None = ...)

class linq.parameters.FloatParameterDefinition(*, id: str = ..., name: str = ..., always_required: bool = False, default: float | None = None, minimum: float | None = None, maximum: float | None = None)

class linq.parameters.IntegerParameterDefinition(*, id: str = ..., name: str = ..., always_required: bool = False, default: int | None = None, minimum: int | None = None, maximum: int | None = None, multiple_of: int | None = None)

class linq.parameters.StringParameterDefinition(*, id: str = ..., name: str = ..., always_required: bool = False, default: str | None = None, is_file_path: bool | None = False, is_directory_path: bool = False)