cromwellLogs: Get log paths associated with one or more workflow ids

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

Description

This will return paths to the standard out and standard error files that were generated during the execution of all calls in a workflow. A call has one or more standard out and standard error logs, depending on if the call was scattered or not. In the latter case, one log is provided for each instance of the call that has been run.

Usage

cromwellLogs(ids, ...)

Arguments

ids	a character vector of Cromwell ids. See cromwellQuery for details of how to query Cromwell for available ids.
...	passed directly to httr 'POST' (for including 'timeouts', 'handles', etc.)

Value

a list of logfile lists. There will be one list item for each id. Each of these list items will contain another list with log outputs from each workflow step in the submitted workflow.

References

https://github.com/broadinstitute/cromwell#get-apiworkflowsversionidlogs

Examples

## Not run: 
res = cromwellQuery(terms=c(status='Succeeded',name='taskName'))
head(res)
loglist = cromwellLogs(res$id)
str(loglist,list.len=5)

## End(Not run)

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