Contents
DownloadVariantSpaceRule
Download variant-space rule
DownloadVariantSpaceRule handles variant-space requests that are directly
downloadable at the requested build -- no liftover needed.
Super class
PolyGenius::Rule -> DownloadVariantSpaceRule
Methods
Public methods
DownloadVariantSpaceRule$new()DownloadVariantSpaceRule$matches()DownloadVariantSpaceRule$inputs()DownloadVariantSpaceRule$requirements()DownloadVariantSpaceRule$run()DownloadVariantSpaceRule$clone()
Method new()
Create the download rule.
Usage
DownloadVariantSpaceRule$new()
Method matches()
Check whether this rule applies to one output spec.
Usage
DownloadVariantSpaceRule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Logical.
Method inputs()
This rule has no upstream dependencies -- the variant space is downloaded directly.
Usage
DownloadVariantSpaceRule$inputs(output.spec)
Arguments
output.spec — Output resource specification (unused).
Returns
Empty list.
Method requirements()
Declare runtime requirements.
Usage
DownloadVariantSpaceRule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification (unused).
inputs — Empty list from inputs() (unused).
Returns
Named list with cores and memory.
Method run()
Download the variant-space file and materialize it as
variants.bed in the resource's own directory.
Usage
DownloadVariantSpaceRule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Empty list (no upstream resources required).
logger — Rule-scoped logger for trace/info messages.
Returns
Named list: data (path), meta, logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
DownloadVariantSpaceRule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.