Help - Workflows at home with CWL

Workflows at home with CWL

Run workflows at home with CWL

Although the BioExcel Building Blocks Workflows website has been built with the aim of executing a set of predefined workflows in our remote servers, the chance of executing these workflows at home is provided as well. In this section is explained how to custom the workflow and get the files for executing it at home via Common Workflow Language.

Custom workflow

First off, users must create a new workflow. We will take the MD Setup as a example.

Step 1: Provide structure

Go to the Create project > From Structure and provide a structure.

Step 2: Check structure

As the example is a MD Setup, after uploading the structure it must be checked. After checking the structure and reviewing the summary checking, we proceed to the following step (settings).

Step 3.1: Settings

In this step, users must choose the workflow to execute and provide parameters according to the selected workflow. These parameters will be integrated in the "Run at home" version of the workflow.

Once the workflow has been chosen and the parameters have been provided, we proceed to the following step (summary settings)

Step 3.2: Summary settings

In this summary we can check all the actions taken in the previous steps, such as the checking or the workflow parameters.

Going down in this same section we will find the Run workflows at home section. In order to get the necessary files for executing the workflow in CWL, we will click the CWL Workflow dropdown button and, once it is deployed, there are four options:

CWL file

Opens in a new tab the CWL file that will run the workflow.

YAML descriptions file

Opens in a new tab the YAML descriptions file with all the configuration parameters (included the ones configured by the users in the settings step) as well as input formats and output paths.


Opens in a modal window the instructions for executing the workflow. The content of this README is in the next section Execute workflow through CWL script.

Download CWL Workflow

Downloads a zip file with all the files needed for the execution of the workflow, included the input(s) file(s) needed.