CWL Tips and Tricks¶
Have a look at the CWL User Guide: Recommended Practices.
Generate yaml file with workflow inputs¶
You can use cwltool --make-template
to generate a yaml file with all the workflow inputs:
cwltool --make-template add_multiply_example.cwl > inputs.yml
inputs.yml
contains:
num1: 0
num2: 0
Use your favorite text editor to set the inputs to appropriate values. Save the file, and use it as input for your workflow:
cwltool add_multiply_example.cwl inputs.yml
Using cwl-runner¶
Install the cwlref-runner
package to set cwl-runner
to cwltool
:
pip install cwlref-runner
If cwl-runner
is set, you can run workflows by typing:
chmod +x workflow.cwl
./workflow.cwl <arguments>
If you have other CWL implementations installed and want cwl-runner
to use one
of these implementations, you should define a symlink that points to the implementation
you want to use; e.g., by manually creating a symlink and adding it to your $PATH
variable, or by using the linux alternatives system.