In labbcb/CromwellClient: R package for consuming Cromwell API

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

CromwellClient consumes Cromwell API.

Setting up Cromwell server locally

Cromwell is a Workflow Management System geared towards scientific workflows.

https://github.com/broadinstitute/cromwell

```{bash, eval=FALSE} wget https://github.com/broadinstitute/cromwell/releases/download/31/cromwell-31.jar java -jar cromwell-31.jar server

<http://localhost:8000>

## Consuming Cromwell API

```r
host <- "http://localhost:8000"
workflow <- system.file("extdata/workflow.wdl", package = "CromwellClient")
inputs <- system.file("extdata/inputs.json", package = "CromwellClient")
job <- submit(host, workflow, inputs)
job

status(job)

outputs(job)
as.data.frame(outputs(job))

logs(job)
as.data.frame(logs(job))

timming(job)

abort(job)

query(host)

Engine

engineStats(host)

engineVersion(host)

engineStatus(host)

Session Information

sessionInfo()

labbcb/CromwellClient documentation built on Aug. 16, 2020, 9:11 p.m.