cwl2nx 0.0.6

Lightweight python module to load, validate and visualize CWL (Common Workflow Language) files through networkx graphs.

CWL2Nx

Lightweight python module to load, validate and visualize CWL (Common Workflow Language) files through networkx graphs. It uses cwl_utils for parsing and validation.

Installation

pip install cwl2nx

Example Usage

You will find an example of workflow in the GitHub repository : workflow_example.cwl.yaml

Straightforward conversion

from cwl2nx import CWLToNetworkxConnector

dir = "workflow_example.cwl.yaml"
dag = CWLToNetworkxConnector(dir).convert_to_networkx() # dag is networkx.DiGraph
print(dag.nodes, dag.edges)

Basic networkx display

Once .cwl is loaded in networkx, you can use any visualization tool to display the dag.

from cwl2nx import CWLToNetworkxConnector
import networkx as nx
import matplotlib.pyplot as plt

dir = "workflow_example.cwl.yaml"
connector = CWLToNetworkxConnector(dir)
dag = connector.convert_to_networkx(datasets_as_nodes=True)
nx.draw_networkx(dag)
plt.show()

Using visualization libraries

You'll need to install dagviz before

Run the cell below in a notebook

from cwl2nx import CWLToNetworkxConnector
import networkx as nx
import dagviz

dir = "workflow_example.cwl.yaml"
connector = CWLToNetworkxConnector(dir)
dag = connector.convert_to_networkx()


dagviz.Dagre(dag)

dagviz.Metro(dag) # github tree dag style

License

Apache 2.0