Loading stepsΒΆ
Before you can create workflows with scriptcwl, you need to load processing steps
(i.e., CommandLineTools
, ExpressionTools
and/or (sub) Workflows
).
To load a directory of .cwl files, type:
from scriptcwl import WorkflowGenerator
with WorkflowGenerator() as wf:
wf.load(steps_dir='/path/to/dir/with/cwl/steps/')
To load a single cwl file, do:
with WorkflowGenerator() as wf:
wf.load(step_file='/path/to/workflow.cwl')
The path to the step_file
can be a local file path or a url.
You can also load a list of step files and directories:
al_my_steps = ['step.cwl', 'url.cwl', '/path/to/directory/']
with WorkflowGenerator() as wf:
wf.load(step_list=all_my_steps)
wf.load()
can be called multiple times. Step files are added to the
steps library one after the other. For every step that is added to the
steps library, a method with the same name is added to the
WorkflowGenerator object. To add a step to the workflow, this method must
be called (examples below).