DownloadReferencePanelRule

Download reference panel rule

Description

Download reference panel rule

Download reference panel rule

Details

DownloadReferencePanelRule handles panel requests where only retrieval is required. After download, split inputs are merged into one fileset and tidied before the reference panel is cached. It does not perform genome-build liftover.

Super class

PolyGenius::Rule -> DownloadReferencePanelRule

Methods

Public methods

• DownloadReferencePanelRule$new()

• DownloadReferencePanelRule$matches()

• DownloadReferencePanelRule$inputs()

• DownloadReferencePanelRule$requirements()

• DownloadReferencePanelRule$run()

• DownloadReferencePanelRule$clone()

Inherited methods

• PolyGenius::Rule$bind()
• PolyGenius::Rule$print()

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Method new()

Create the download rule.

Usage

DownloadReferencePanelRule$new()

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Method matches()

Check whether this rule applies to one output spec.

Usage

DownloadReferencePanelRule$matches(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Logical.

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Method inputs()

Build dependency inputs.

Usage

DownloadReferencePanelRule$inputs(output.spec)

Arguments

output.spec

Output resource specification.

Returns

Named list of dependency specs.

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Method requirements()

Declare runtime requirements.

Usage

DownloadReferencePanelRule$requirements(output.spec, inputs)

Arguments

output.spec

Output resource specification.

inputs

Bound input values.

Returns

Named list with cores and memory.

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Method run()

Execute panel download and unpacking.

Usage

DownloadReferencePanelRule$run(output.spec, inputs, logger)

Arguments

output.spec

Output resource specification.

inputs

Bound input values.

logger

Rule logger.

Returns

Rule result list with data, meta, and logs.

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Method clone()

The objects of this class are cloneable with this method.

Usage

DownloadReferencePanelRule$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.