cwl

Execute workflow through CWL script

To execute the workflow through a CWL script, please follow the next steps:

Workflow files

Below you can find the list of all the needed files for executing this workflow:

• workflow.cwl: the CWL file with all the steps to execute this workflow.
• workflow_input_descriptions.yml: the configuration file with the I/O dependencies and settings for each step of the workflow.

Requirements

For executing a BioBB workflow in CWL, you should have git, cwltool and docker installed in your computer.

Biobb adapters

Please be sure to have the biobb_adapters folder at the same level where the workflow.cwl and workflow_input_descriptions.yml files are.

Run workflow

After that, the only thing left is to run the workflow:

cwltool workflow.cwl workflow_input_descriptions.yml

Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a few minutes to several hours. The workflow progress will be shown in your terminal.

Get output results

Once the workflow is finished, you will have all the files generated in every step in the same folder.