cromwellBatch: Submit a cromwell batch job

In seandavi/wdlRunR: Interact with the Broad Institute Cromwell workflow manager

Description

This function submits a set of one or more inputs to cromwell. It is much more efficient than submitting a single job at a time. See the cromwell batch API documentation for details.

Usage

cromwellBatch(wdlSource, workflowInputs, customLabels = NULL,
  workflowOptions = NULL, timeout = 120, ...)

Arguments

wdlSource	Represents the WDL A string (character vector of length 1) or an upload_file object. See details below.
workflowInputs	A data.frame that will be coerced to a json array or a JSON string (as a character vector of length 1), or an upload_file object. See details below.
customLabels	A named character vector with key-value pairs to assign to all batch tasks.
workflowOptions	A list, a JSON string (as a character vector of length 1, or an upload_file object. See details below.
timeout	The number of seconds to wait for a response. Batch jobs can take quite some time for cromwell to process, so this will typically need to be set to a large value to allow for a completed response.
...	passed directly to httr 'POST' (for including 'timeouts', 'handles', etc.)

Details

TODO details

Value

If a timeout does not occur (this is pretty common....), then a list that contains the submission status.

seandavi/wdlRunR documentation built on Oct. 28, 2021, 12:42 a.m.