sbgr (version 1.0.0)

task_run: Runs a task as a part of a project

Description

Runs a task as a part of a project.

Usage

task_run(auth_token = NULL, project_id = NULL, task_details = NULL, ...)

Arguments

auth_token

auth token

project_id

ID of a project you want to access.

task_details

A list with the following components:

• pipeline_id - ID of the pipeline you wish to execute
• pipeline_revision - Revision of the pipeline you wish to execute. If not specified, latest revision is used.
• name - Name of the task you wish to execute
• description - Description of the task you wish to execute
• inputs - Named list containing mappings of pipeline input node ID to file IDs. Note that file IDs always need to be specified as an list, even if empty or with one element.
• parameters - Named list containing mappings of node IDs to apps specific parameters. Note that parameters are always specified as an list, even if empty or with one element.

...

parameters passed to sbgapi function

Value

parsed list of the returned json

Details

All the details, including the pipeline ID and runtime parameters, are specified via a list. See the example for details.

Examples

token = '58aeb140-1970-0130-6386-001f5b34aa78'
details = list(
  'name' = 'Test 2 of C. Elegans VC',
  'description' = 'Testing Caenorhabditis elegans Exome Variant Calling',
  'pipeline_id' = '422',
  'inputs' = list('309485' = 13645,
                  '317344' = 13646,
                  '318662' = 13645,
                  '699018' = 13647),
  'parameters' = list('393463' = list('read_trimming_qual' = 30,
                                      'rg_seq_tech' = 'Illumina'),
                      '677492' = list()))

req = task_run(token,
                project_id = '7f7a72d0-da77-4f51-9416-99f14f7316ab',
                task_details = details)