Common Workflow Language building blocks

AnyLiteralType

Generic identifier name pattern.

CUDAComputeCapabilityArray

CWLVersion

CWLDocumentation

CWLIntent

Describes how to decompose the scattered input into a discrete set of jobs. When 'dotproduct', specifies that each of the input arrays are aligned and one element taken from each array to construct each job. It is an error if all input arrays are of different length. When 'nested_crossproduct', specifies the Cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output must be nested arrays for each level of scattering, in the order that the input arrays are listed in the scatter field. When 'flat_crossproduct', specifies the Cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output arrays must be flattened to a single level, but otherwise listed in the order that the input arrays are listed in the scatter field.

Command called in the docker image or on shell according to requirements and hints specifications. Can be omitted if already defined in the docker image.

When combined with 'InlineJavascriptRequirement', this field allows runtime parameter references (see also: https://www.commonwl.org/v1.2/CommandLineTool.html#Expression).

CWLDefaultObject

CWLDefaultLocation

CWLTypeSymbolValues

LoadListingEnum

Represents an '$import' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported.

Generic schema to allow alternative CWL requirements/hints not explicitly defined in schemas.

Indicates that the value passed to this CWL input will be redirected to the standard input stream of the command. Can be defined for only one input and must not be combined with 'stdin' at the root of the CWL document.

Keywords applied to the process for search and categorization purposes.

Indicates that the data pushed to the standard error stream by the command will be redirected to this CWL output. Can be defined for only one output. If combined with 'stderr' at the root of the CWL document, that definition will indicate the desired name of the output file where the error stream will be written to. A random name will be applied for the file of this output unless otherwise specified.

Indicates that the data pushed to the standard output stream by the command will be redirected to this CWL output. Can be defined for only one output. If combined with 'stdout' at the root of the CWL document, that definition will indicate the desired name of the output file where the output stream will be written to. A random name will be applied for the file of this output unless otherwise specified.

Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolation (see also: https://www.commonwl.org/v1.2/CommandLineTool.html#InlineJavascriptRequirement).

ShellCommandRequirement

Indicates that the 'Workflow' must support multiple inbound data links listed in the 'source' field of 'WorkflowStepInput'.

If 'inplaceUpdate' is true, then an implementation supporting this feature may permit tools to directly update files with 'writable: true' in 'InitialWorkDirRequirement'. That is, as an optimization, files may be destructively modified in place as opposed to copied and updated (see also: https://www.commonwl.org/v1.2/CommandLineTool.html#InplaceUpdateRequirement).

Indicates that the 'Workflow' must support the 'valueFrom' field of 'WorkflowStepInput'.

DockerRequirement

A 'scatter' operation specifies that the associated Workflow step should execute separately over a list of input elements. Each job making up a scatter operation is independent and may be executed concurrently (see also: https://www.commonwl.org/v1.2/Workflow.html#WorkflowStep).

Indicates that the 'Workflow' must support nested workflows in the 'run' field of 'WorkflowStep'.

Field type definition.

CWLTypeRecordFieldsItem

CWLTypeRecordRefPattern

CWLWorkflowClass

LinkMergeMethod

Checksum

ReferenceURL

An item quantity that can also represent a proportion of use by resources.

SoftwarePackageSpecs

Hint indicating that the Application Package corresponds to a builtin process of this instance. (note: can only be an 'hint' as it is unofficial CWL specification).

Reference to the process identifier.

IdentifierArray

The compute capability supported by the GPU hardware. * If this is a single value, it defines only the minimum compute capability. GPUs with higher capability are also accepted. * If it is an array value, then only select GPUs with compute capabilities that explicitly appear in the array. See https://docs.nvidia.com/deploy/cuda-compatibility/#faq and https://docs.nvidia.com/cuda/cuda-c-best-practices-guide/index.html#cuda-compute-capability for details.

CWLFileOnlyParameters

EnvVarRequirement

Defines how to specify the input for the command.

NetworkAccessRequirement

Defines how to retrieve the output result from the command.

Set an upper limit on the execution time of a CommandLineTool. A CommandLineTool whose execution duration exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions. The execution duration excludes external operations, such as staging of files, pulling a docker image etc., and only counts wall-time for the execution of the command line itself.

For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution. If 'WorkReuse' is not specified, correct tools should assume it is enabled by default.

Default value of input if not provided for task execution.

CWLTypeSymbols

CWLDirectoryOnlyParameters

Specify the desired behavior for loading the listing field of a 'Directory' object for use by expressions (see also: https://www.commonwl.org/v1.2/CommandLineTool.html#LoadListingRequirement).

CWLInputStdInObjectType

CWLMetadata

CWLOutputStdErr

CWLOutputStdOut

CWLTypeRecordSchema

An IRI with minimally a '{Record}' identifier to look for a schema definition locally or remotely. The identifier resolution is performed accordingly to the specified reference and as described in https://www.commonwl.org/v1.2/SchemaSalad.html#Identifier_resolution.

CWLWorkflowStepInputBase

InitialWorkDirRequirement

Hint indicating that the Application Package corresponds to an OGC API - Processes provider that should be remotely executed and monitored by this instance. (note: can only be an 'hint' as it is unofficial CWL specification).

SoftwarePackage

Hint indicating that the Application Package corresponds to a WPS-1 provider process that should be remotely executed and monitored by this instance. (note: can only be an ''hint'' as it is unofficial CWL specification).

Maximum reserved number of CPU cores. See 'coresMin' for discussion about fractional CPU requests.

Minimum reserved number of CPU cores. May be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 ~ 3). Processes can only share a core allocation if the sum of each of their 'ramMax', 'tmpdirMax', and 'outdirMax' requests also do not exceed the capacity of the node. Processes sharing a core must have the same level of isolation (typically a container or VM) that they would normally have. The reported number of CPU cores reserved for the process, which is available to expressions on the 'CommandLineTool' as 'runtime.cores', must be a non-zero integer, and may be calculated by rounding up the cores request to the next whole number. Scheduling systems may allocate fractional CPU resources by setting quotas or scheduling weights. Scheduling systems that do not support fractional CPUs may round up the request to the next whole number.

Maximum reserved filesystem based storage for the designated output directory in mebibytes (2**20). See 'outdirMin' for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated output directory in mebibytes (2**20). May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the 'CommandLineTool' as 'runtime.outdirSize', must be a non-zero integer.

Maximum reserved RAM in mebibytes (2**20). See 'ramMin' for discussion about fractional RAM requests.

Minimum reserved RAM in mebibytes (2**20). May be a fractional value. If so, the actual RAM request must be rounded up to the next whole number. The reported amount of RAM reserved for the process, which is available to expressions on the 'CommandLineTool' as 'runtime.ram', must be a non-zero integer.

Maximum reserved filesystem based storage for the designated temporary directory in mebibytes (2**20). See 'tmpdirMin' for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated temporary directory in mebibytes (2**20). May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the 'CommandLineTool' as 'runtime.tmpdirSize', must be a non-zero integer.

One or more input identifier of an application step within a Workflow were an array-based input to that Workflow should be scattered across multiple instances of the step application.

CWLWorkflowStepId

cwltool:CUDARequirement

Parameters that are only valid when 'type' or 'items' evaluates to 'File'.

Base arguments passed to the command.

CWLWorkflowStepInputDefault

CWLDefaultTypedConditional

CWLTypeEnum

Parameters that are only valid when 'type' or 'items' evaluates to 'Directory'.

CWLInputStdIn

SoftwareRequirement

CWLHintsItemExtras

CWLHintsMapExtras

Specify basic hardware resource requirements (see also: https://www.commonwl.org/v1.2/CommandLineTool.html#ResourceRequirement).

Mapping of Workflow step inputs to nested CWL tool definitions inputs or outputs.

CWLWorkflowStepInItem

CWLType

Mapping of Workflow step inputs to nested CWL tool definitions inputs or outputs.

CWLInputItemBase

CWLInputObject

Output specification. Note that multiple formats are supported and not all specification variants or parameters are presented here. Please refer to official CWL documentation for more details (https://www.commonwl.org).

CWLOutputObject

CWLTypeRecordArray

CWLTypeRecordFieldDef

Input specification. Note that multiple formats are supported and not all specification variants or parameters are presented here. Please refer to official CWL documentation for more details (https://www.commonwl.org).

All outputs produced by the Application Package.

SchemaDefRequirement

All inputs available to the Application Package.

CWLRequirementsItem

CWLRequirementsMap

CWLHintsItem

Explicit requirement to execute the application package.

Non-failing additional hints that can help resolve extra requirements.

Direct CWL definition instead of the graph representation.

CWLGraphItemBase

CWLAtomic

CWLAtomicNested

CWLGraphItem

CWLWorkflowStepObject

CWLGraph

CWLWorkflowStepItem

CWLWorkflowBase

CWLWorkflow

CWL