cromwellBatch: Submit a cromwell batch job

Description Usage Arguments Details Value

View source: R/api.R

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

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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.