CfnWorkflowPropsMixin

class aws_cdk.mixins_preview.aws_omics.mixins.CfnWorkflowPropsMixin(props, *, strategy=None)

Bases: Mixin

Creates a private workflow. Before you create a private workflow, you must create and configure these required resources:.

  • Workflow definition file: A workflow definition file written in WDL, Nextflow, or CWL. The workflow definition specifies the inputs and outputs for runs that use the workflow. It also includes specifications for the runs and run tasks for your workflow, including compute and memory requirements. The workflow definition file must be in .zip format. For more information, see Workflow definition files in AWS HealthOmics.

  • You can use Amazon Q CLI to build and validate your workflow definition files in WDL, Nextflow, and CWL. For more information, see Example prompts for Amazon Q CLI and the AWS HealthOmics Agentic generative AI tutorial on GitHub.

  • (Optional) Parameter template file: A parameter template file written in JSON. Create the file to define the run parameters, or AWS HealthOmics generates the parameter template for you. For more information, see Parameter template files for HealthOmics workflows .

  • ECR container images: Create container images for the workflow in a private ECR repository, or synchronize images from a supported upstream registry with your Amazon ECR private repository.

  • (Optional) Sentieon licenses: Request a Sentieon license to use the Sentieon software in private workflows.

For more information, see Creating or updating a private workflow in AWS HealthOmics in the AWS HealthOmics User Guide .

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-resource-omics-workflow.html

CloudformationResource:

AWS::Omics::Workflow

Mixin:

true

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview import mixins
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

cfn_workflow_props_mixin = omics_mixins.CfnWorkflowPropsMixin(omics_mixins.CfnWorkflowMixinProps(
    accelerators="accelerators",
    container_registry_map=omics_mixins.CfnWorkflowPropsMixin.ContainerRegistryMapProperty(
        image_mappings=[omics_mixins.CfnWorkflowPropsMixin.ImageMappingProperty(
            destination_image="destinationImage",
            source_image="sourceImage"
        )],
        registry_mappings=[omics_mixins.CfnWorkflowPropsMixin.RegistryMappingProperty(
            ecr_account_id="ecrAccountId",
            ecr_repository_prefix="ecrRepositoryPrefix",
            upstream_registry_url="upstreamRegistryUrl",
            upstream_repository_prefix="upstreamRepositoryPrefix"
        )]
    ),
    container_registry_map_uri="containerRegistryMapUri",
    definition_repository=omics_mixins.CfnWorkflowPropsMixin.DefinitionRepositoryProperty(
        connection_arn="connectionArn",
        exclude_file_patterns=["excludeFilePatterns"],
        full_repository_id="fullRepositoryId",
        source_reference=omics_mixins.CfnWorkflowPropsMixin.SourceReferenceProperty(
            type="type",
            value="value"
        )
    ),
    definition_uri="definitionUri",
    description="description",
    engine="engine",
    main="main",
    name="name",
    parameter_template={
        "parameter_template_key": omics_mixins.CfnWorkflowPropsMixin.WorkflowParameterProperty(
            description="description",
            optional=False
        )
    },
    parameter_template_path="parameterTemplatePath",
    readme_markdown="readmeMarkdown",
    readme_path="readmePath",
    readme_uri="readmeUri",
    storage_capacity=123,
    storage_type="storageType",
    tags={
        "tags_key": "tags"
    },
    workflow_bucket_owner_id="workflowBucketOwnerId"
),
    strategy=mixins.PropertyMergeStrategy.OVERRIDE
)

Create a mixin to apply properties to AWS::Omics::Workflow.

Parameters:

  • props (Union[CfnWorkflowMixinProps, Dict[str, Any]]) – L1 properties to apply.

  • strategy (Optional[PropertyMergeStrategy]) – (experimental) Strategy for merging nested properties. Default: - PropertyMergeStrategy.MERGE

Methods

apply_to(construct)

Apply the mixin properties to the construct.

Parameters:

construct (IConstruct)

Return type:

IConstruct

supports(construct)

Check if this mixin supports the given construct.

Parameters:

construct (IConstruct)

Return type:

bool

Attributes

CFN_PROPERTY_KEYS = ['accelerators', 'containerRegistryMap', 'containerRegistryMapUri', 'definitionRepository', 'definitionUri', 'description', 'engine', 'main', 'name', 'parameterTemplate', 'parameterTemplatePath', 'readmeMarkdown', 'readmePath', 'readmeUri', 'storageCapacity', 'storageType', 'tags', 'workflowBucketOwnerId']

Static Methods

classmethod is_mixin(x)

(experimental) Checks if x is a Mixin.

Parameters:

x (Any) – Any object.

Return type:

bool

Returns:

true if x is an object created from a class which extends Mixin.

Stability:

experimental

ContainerRegistryMapProperty

class CfnWorkflowPropsMixin.ContainerRegistryMapProperty(*, image_mappings=None, registry_mappings=None)

Bases: object

Use a container registry map to specify mappings between the ECR private repository and one or more upstream registries.

For more information, see Container images in the AWS HealthOmics User Guide .

Parameters:

  • image_mappings (Union[IResolvable, Sequence[Union[IResolvable, ImageMappingProperty, Dict[str, Any]]], None]) – Image mappings specify path mappings between the ECR private repository and their corresponding external repositories.

  • registry_mappings (Union[IResolvable, Sequence[Union[IResolvable, RegistryMappingProperty, Dict[str, Any]]], None]) – Mapping that provides the ECR repository path where upstream container images are pulled and synchronized.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-containerregistrymap.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

container_registry_map_property = omics_mixins.CfnWorkflowPropsMixin.ContainerRegistryMapProperty(
    image_mappings=[omics_mixins.CfnWorkflowPropsMixin.ImageMappingProperty(
        destination_image="destinationImage",
        source_image="sourceImage"
    )],
    registry_mappings=[omics_mixins.CfnWorkflowPropsMixin.RegistryMappingProperty(
        ecr_account_id="ecrAccountId",
        ecr_repository_prefix="ecrRepositoryPrefix",
        upstream_registry_url="upstreamRegistryUrl",
        upstream_repository_prefix="upstreamRepositoryPrefix"
    )]
)

Attributes

image_mappings

Image mappings specify path mappings between the ECR private repository and their corresponding external repositories.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-containerregistrymap.html#cfn-omics-workflow-containerregistrymap-imagemappings

registry_mappings

Mapping that provides the ECR repository path where upstream container images are pulled and synchronized.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-containerregistrymap.html#cfn-omics-workflow-containerregistrymap-registrymappings

DefinitionRepositoryProperty

class CfnWorkflowPropsMixin.DefinitionRepositoryProperty(*, connection_arn=None, exclude_file_patterns=None, full_repository_id=None, source_reference=None)

Bases: object

Contains information about a source code repository that hosts the workflow definition files.

Parameters:

  • connection_arn (Optional[str]) – The Amazon Resource Name (ARN) of the connection to the source code repository.

  • exclude_file_patterns (Optional[Sequence[str]]) – A list of file patterns to exclude when retrieving the workflow definition from the repository.

  • full_repository_id (Optional[str]) – The full repository identifier, including the repository owner and name. For example, ‘repository-owner/repository-name’.

  • source_reference (Union[IResolvable, SourceReferenceProperty, Dict[str, Any], None]) – The source reference for the repository, such as a branch name, tag, or commit ID.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-definitionrepository.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

definition_repository_property = omics_mixins.CfnWorkflowPropsMixin.DefinitionRepositoryProperty(
    connection_arn="connectionArn",
    exclude_file_patterns=["excludeFilePatterns"],
    full_repository_id="fullRepositoryId",
    source_reference=omics_mixins.CfnWorkflowPropsMixin.SourceReferenceProperty(
        type="type",
        value="value"
    )
)

Attributes

connection_arn

The Amazon Resource Name (ARN) of the connection to the source code repository.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-definitionrepository.html#cfn-omics-workflow-definitionrepository-connectionarn

exclude_file_patterns

A list of file patterns to exclude when retrieving the workflow definition from the repository.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-definitionrepository.html#cfn-omics-workflow-definitionrepository-excludefilepatterns

full_repository_id

The full repository identifier, including the repository owner and name.

For example, ‘repository-owner/repository-name’.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-definitionrepository.html#cfn-omics-workflow-definitionrepository-fullrepositoryid

source_reference

The source reference for the repository, such as a branch name, tag, or commit ID.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-definitionrepository.html#cfn-omics-workflow-definitionrepository-sourcereference

ImageMappingProperty

class CfnWorkflowPropsMixin.ImageMappingProperty(*, destination_image=None, source_image=None)

Bases: object

Specifies image mappings that workflow tasks can use.

For example, you can replace all the task references of a public image to use an equivalent image in your private ECR repository. You can use image mappings with upstream registries that don’t support pull through cache. You need to manually synchronize the upstream registry with your private repository.

Parameters:

  • destination_image (Optional[str]) – Specifies the URI of the corresponding image in the private ECR registry.

  • source_image (Optional[str]) – Specifies the URI of the source image in the upstream registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-imagemapping.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

image_mapping_property = omics_mixins.CfnWorkflowPropsMixin.ImageMappingProperty(
    destination_image="destinationImage",
    source_image="sourceImage"
)

Attributes

destination_image

Specifies the URI of the corresponding image in the private ECR registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-imagemapping.html#cfn-omics-workflow-imagemapping-destinationimage

source_image

Specifies the URI of the source image in the upstream registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-imagemapping.html#cfn-omics-workflow-imagemapping-sourceimage

RegistryMappingProperty

class CfnWorkflowPropsMixin.RegistryMappingProperty(*, ecr_account_id=None, ecr_repository_prefix=None, upstream_registry_url=None, upstream_repository_prefix=None)

Bases: object

If you are using the ECR pull through cache feature, the registry mapping maps between the ECR repository and the upstream registry where container images are pulled and synchronized.

Parameters:

  • ecr_account_id (Optional[str]) – Account ID of the account that owns the upstream container image.

  • ecr_repository_prefix (Optional[str]) – The repository prefix to use in the ECR private repository.

  • upstream_registry_url (Optional[str]) – The URI of the upstream registry.

  • upstream_repository_prefix (Optional[str]) – The repository prefix of the corresponding repository in the upstream registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-registrymapping.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

registry_mapping_property = omics_mixins.CfnWorkflowPropsMixin.RegistryMappingProperty(
    ecr_account_id="ecrAccountId",
    ecr_repository_prefix="ecrRepositoryPrefix",
    upstream_registry_url="upstreamRegistryUrl",
    upstream_repository_prefix="upstreamRepositoryPrefix"
)

Attributes

ecr_account_id

Account ID of the account that owns the upstream container image.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-registrymapping.html#cfn-omics-workflow-registrymapping-ecraccountid

ecr_repository_prefix

The repository prefix to use in the ECR private repository.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-registrymapping.html#cfn-omics-workflow-registrymapping-ecrrepositoryprefix

upstream_registry_url

The URI of the upstream registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-registrymapping.html#cfn-omics-workflow-registrymapping-upstreamregistryurl

upstream_repository_prefix

The repository prefix of the corresponding repository in the upstream registry.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-registrymapping.html#cfn-omics-workflow-registrymapping-upstreamrepositoryprefix

SourceReferenceProperty

class CfnWorkflowPropsMixin.SourceReferenceProperty(*, type=None, value=None)

Bases: object

Contains information about the source reference in a code repository, such as a branch, tag, or commit.

Parameters:

  • type (Optional[str]) – The type of source reference, such as branch, tag, or commit.

  • value (Optional[str]) – The value of the source reference, such as the branch name, tag name, or commit ID.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-sourcereference.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

source_reference_property = omics_mixins.CfnWorkflowPropsMixin.SourceReferenceProperty(
    type="type",
    value="value"
)

Attributes

type

The type of source reference, such as branch, tag, or commit.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-sourcereference.html#cfn-omics-workflow-sourcereference-type

value

The value of the source reference, such as the branch name, tag name, or commit ID.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-sourcereference.html#cfn-omics-workflow-sourcereference-value

WorkflowParameterProperty

class CfnWorkflowPropsMixin.WorkflowParameterProperty(*, description=None, optional=None)

Bases: object

A workflow parameter.

Parameters:

  • description (Optional[str]) – The parameter’s description.

  • optional (Union[bool, IResolvable, None]) – Whether the parameter is optional.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-workflowparameter.html

ExampleMetadata:

fixture=_generated

Example:

# The code below shows an example of how to instantiate this type.
# The values are placeholders you should change.
from aws_cdk.mixins_preview.aws_omics import mixins as omics_mixins

workflow_parameter_property = omics_mixins.CfnWorkflowPropsMixin.WorkflowParameterProperty(
    description="description",
    optional=False
)

Attributes

description

The parameter’s description.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-workflowparameter.html#cfn-omics-workflow-workflowparameter-description

optional

Whether the parameter is optional.

See:

http://docs.aws.amazon.com/AWSCloudFormation/latest/UserGuide/aws-properties-omics-workflow-workflowparameter.html#cfn-omics-workflow-workflowparameter-optional