AnVIL workspace

getOutput

R Documentation

Download output files from Terra

Description

Download output files from Terra

Usage

getOutput(
  workspaceName,
  submissionId = NULL,
  keyword = NULL,
  dest_dir = ".",
  dry = TRUE
)

Arguments

`workspaceName`	Name of the workspace
`submissionId`	Submission Id. If it's not provided, the most recent submission id with the 'succeeded' status will be used.
`keyword`	A character string containing a regular expression to be matched in the output file name. Under the default `NULL`, all the outputs from the workflow, including log files, will be returned.
`dest_dir`	Path to the directory where downloaded files are saved
`dry`	To download the output data, set `dry = FALSE`.

Value

If "dry=TRUE", this function will return a data frame with two columns named 'filename' and 'name'.

filename: Name of the actual output files.
name: Name of the output defined in your workflow script. This is how configuration refers the outputs.

Examples

library(AnVILBase)
if (
    gcloud_exists() && identical(avplatform_namespace(), "AnVILGCP") &&
    nzchar(avworkspace_name())
) {
getOutput(workspaceName = "Bioconductor-Workflow-DESeq2")
}

shbrief/RunTerraWorkflow documentation built on Oct. 31, 2024, 1:22 p.m.