blue_cwl.core.cwl¶

CWL workflow construction module.

Classes

`CommandInputArraySchema`(*, items, type[, ...])	CommandInputArraySchema.
`CommandInputParameter`(*, id[, label, doc, ...])	CommandInputParameter shema.
`CommandLineBinding`(*[, position, prefix, ...])	Dataclass for a command line's tool input binding.
`CommandLineTool`(*, cwlVersion[, id, ...])	Dataclass for a command line tool's output.
`CommandOutputBinding`(*[, glob])	CommandOutputbinding schema.
`CommandOutputParameter`(*[, id, label, doc, ...])	CommandOutputParameter schema.
`Config`(*, inputs)	Dataclass for cwl config.
`ConfigInput`(*, type, value)	Dataclass for config's input entries.
`InputArraySchema`(*, items, type[, label, ...])	InputArraySchema.
`Workflow`(*, cwlVersion[, id])	Dataclass for an entire workflow.
`WorkflowInputParameter`(*, type[, id, doc, ...])	WorkflowInputParameter schema.
`WorkflowOutputParameter`(*[, id, label, doc])	Dataclass for a workflow's output.
`WorkflowStep`(*, id, inputs, outputs, run)	Dataclass for a workflow's step.
`WorkflowStepInput`(*, id[, label, source, ...])	Dataclass for a workflow'steps input.

class blue_cwl.core.cwl.CommandInputArraySchema(*, items: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], type: Literal['array'], label: str | None = None, doc: str | None = None, name: str | None = None, inputBinding: CommandLineBinding | None = None)¶

CommandInputArraySchema.

See: https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputArraySchema

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.CommandInputParameter(*, id: str, label: str | None = None, doc: str | None = None, inputBinding: CommandLineBinding | None = None, default: Any = None, type: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'] | CommandInputArraySchema)¶

CommandInputParameter shema.

See: https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputParameter

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.CommandLineBinding(*, position: int = 0, prefix: str | None = None, separate: bool = True, itemSeparator: str = ' ')¶

Dataclass for a command line’s tool input binding.

position¶

Integer signifying the position in the command line. Default 0.

Type:: int

prefix¶

Optional prefix for named argument.

Type:: str | None

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.CommandLineTool(*, cwlVersion: Literal['v1.2'], id: str = 'CommandLineTool', baseCommand: list[str], inputs: dict[str, CommandInputParameter], outputs: dict[str, CommandOutputParameter], environment: dict | None = None, executor: LocalExecutor | SallocExecutor | None = None, label: str | None = None, stdout: str | None = None)¶

Dataclass for a command line tool’s output.

id¶

The unique identifier for this object.

Type:: str

label¶

A short, human-readable label of this object.

Type:: str | None

baseCommand¶

Specifies the program to execute.

Type:: list[str]

inputs¶

Defines the input parameters of the process.

Type:: dict[str, blue_cwl.core.cwl.CommandInputParameter]

outputs¶

Defines the parameters representing the output of the process.

Type:: dict[str, blue_cwl.core.cwl.CommandOutputParameter]

stdout¶

Capture the command’s standard output stream to a file written to the designated output directory.

Type:: str | None

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

make(input_values: dict)¶: Make an executable process out of the template and the inputs.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.CommandOutputBinding(*, glob: str | None = None)¶

CommandOutputbinding schema.

See: https://www.commonwl.org/v1.2/CommandLineTool.html#CommandOutputBinding

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.CommandOutputParameter(*, id: str | None = None, type: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], label: str | None = None, doc: str | None = None, outputBinding: CommandOutputBinding | None = None)¶

CommandOutputParameter schema.

See https://www.commonwl.org/v1.2/CommandLineTool.html#CommandOutputParameter

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.Config(*, inputs: dict[str, ConfigInput])¶

Dataclass for cwl config.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.ConfigInput(*, type: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], value: str)¶

Dataclass for config’s input entries.

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.InputArraySchema(*, items: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], type: Literal['array'], label: str | None = None, doc: str | None = None, name: str | None = None)¶

InputArraySchema.

See: https://www.commonwl.org/v1.2/Workflow.html#InputArraySchema

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.Workflow(*, cwlVersion: str, id: str = 'Workflow', label: str, inputs: dict[str, WorkflowInputParameter], outputs: dict[str, WorkflowOutputParameter], steps: list[WorkflowStep])¶

Dataclass for an entire workflow.

cwlVersion¶

Version of the cwl specication.

Type:: str

id¶

Name of the workflow.

Type:: str

label¶

Description of the workflow.

Type:: str

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

get_step_by_name(name)¶: Return the workflow step with given name.

get_step_source_names(name: str) → list[str]¶: Get source names for workflow step.

iter_steps()¶: Iterate over steps.

make(input_values)¶: Make a concretized workflow process.

make_workflow_step(step_name, input_values, sources)¶: Make workflow step.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

show_image()¶: Show workflow graph image.

step_names() → list[str]¶: Return the names of the workflow steps.

write_image(filepath)¶: Save workflow graph as an image.

class blue_cwl.core.cwl.WorkflowInputParameter(*, type: InputArraySchema | Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], id: str | None = None, doc: str | None = None, label: str | None = None, default: Any = None)¶

WorkflowInputParameter schema.

See: https://www.commonwl.org/v1.2/Workflow.html#WorkflowInputParameter

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class blue_cwl.core.cwl.WorkflowOutputParameter(*, id: str | None = None, type: Literal['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File', 'Directory', 'stdin', 'stdout', 'stderr', 'Any', 'NexusType'], label: str | None = None, doc: str | None = None, outputSource: str)¶

Dataclass for a workflow’s output.

See: https://www.commonwl.org/v1.2/Workflow.html#WorkflowOutputParameter

type¶

The type of the output.

Type:: Literal[‘null’, ‘boolean’, ‘int’, ‘long’, ‘float’, ‘double’, ‘string’, ‘File’, ‘Directory’, ‘stdin’, ‘stdout’, ‘stderr’, ‘Any’, ‘NexusType’]

outputSource¶

Type:: str

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

split_source_output() → list[str]¶: Return step and output names for source.

class blue_cwl.core.cwl.WorkflowStep(*, id: str, inputs: dict[str, WorkflowStepInput], outputs: list[str], run: CommandLineTool)¶

Dataclass for a workflow’s step.

id¶

The unique identifier for this object.

Type:: str

inputs¶

The inputs of the step.

Type:: dict[str, blue_cwl.core.cwl.WorkflowStepInput]

outputs¶

The outputs of the step.

Type:: list[str]

run¶

The comannd line tool executed by the step.

Type:: blue_cwl.core.cwl.CommandLineTool

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

Dataclass for a workflow’steps input.

See https://www.commonwl.org/v1.2/Workflow.html#WorkflowStepInput

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'extra': 'forbid', 'frozen': True, 'strict': True, 'validate_assignment': True}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

split_source_output() → list[tuple[str | None, str]] | None¶: Split source and return source and outputs names if any.