Contents
DownloadReferencePanelRule
Download reference panel rule
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()
Method new()
Create the download rule.
Usage
DownloadReferencePanelRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
DownloadReferencePanelRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
Build dependency inputs.
Usage
DownloadReferencePanelRule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list of dependency specs.
Method requirements()
Declare runtime requirements.
Usage
DownloadReferencePanelRule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification.
inputs — Bound input values.
Returns
Named list with cores and memory.
Method run()
Execute panel download and unpacking.
Usage
DownloadReferencePanelRule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Bound input values.
logger — Rule logger.
Returns
Rule result list with data, meta, and logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
DownloadReferencePanelRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.