heliumdatacommons/cwl_workflows

Name: cwl_workflows

Owner: heliumdatacommons

Description: Example CWL Workflows that run on the PIVOT architecture.

Created: 2018-05-07 12:30:11.0

Updated: 2018-05-07 15:01:14.0

Pushed: 2018-05-07 15:01:13.0

Homepage: null

Size: 4

Language: Common Workflow Language

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

User	Email	Most Recent Commit	# Commits

README

cwl_workflows

Example CWL Workflows that run on the PIVOT architecture.

How to run workflows

Data commons execution assumes you ae executing commands in the Data Commons Docker image.

bin/helium run base -cwl -U <username> -P <password>

The script ./bin/helium is located here.

Touch Job

 /renci/irods/home/chris_ball/my-tar-cwl/
ltool --data-commons ../../../../../GitRepos/dc-cwl_workflows/workflows/complex-workflow/touch.cwl ../../../../../GitRepos/dc-cwl_workflows/workflows/complex-workflow/touch-job.yml

Complex Workflow

Local execution:

 workflows/complex-workflow/data
ltool ../complex-workflow-1.cwl ../complex-workflow-1-job-local.yml

Will create workflows/complex-workflow/data/test.tar file with 8 files in the archive.

Data Commons execution:

 /renci/irods/home/chris_ball/my-tar-cwl/
ltool --data-commons /GitRepos/dc-cwl_workflows/workflows/complex-workflow/complex-workflow-1.cwl /GitRepos/dc-cwl_workflows/workflows/complex-workflow/complex-workflow-1-job-datacommons.yml
ool --data-commons ../../../../../GitRepos/dc-cwl_workflows/workflows/complex-workflow/complex-workflow-1.cwl ../../../../../GitRepos/dc-cwl_workflows/workflows/complex-workflow/complex-workflow-1-job-datacommons.yml