cwl2nx 0.0.12

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. It also contains a CLI app to quickly visualize cwl files.

Installation

pip install cwl2nx

Note : to use cwl2nx as a CLI app only, you may prefer to use pipx :

pip install pipx
pipx install cwl2nx

Example Usage

You will find an example of workflow in the GitHub repository : workflow_example.cwl.yaml. Other examples can be found here : https://workflowhub.org

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)

Using dagviz

You'll need to install dagviz before

/!\ you need to run the code below in a jupyter 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

Visualization in the terminal

To get a string representing the graph (code from: https://github.com/ctongfei/py-dagviz):

from cwl2nx import cwl_to_str

dir = "workflow_example.cwl.yaml"
print(cwl_to_str(dir))

output :

• input_file_1.json
│ • parameter.py
│ │ • config.yaml
╰─│─┴─• init_task
  │   ╰─• init_task/initialized_dataset.json
  ├─────┼─• inter_task_1
  │     ├─│─• inter_task_2
  │     │ ╰─│─• inter_task_1/output_inter_1
  │     │   ╰─│─• inter_task_2/output_inter_2
  ╰─────│─────┴─┴─• end_task
        │         ╰─• end_task/output.csv
        │           ╰─• wf_output
        ╰─• wf_output_2

CLI app

Just run :

cwl2nx <path_to_cwl>

run cwl2nx --help to get full documentation

• green: WorkflowInputParameter
• yellow: WorkflowStep
• blue: WorkflowStepInput
• pink / magenta : WorkflowStepOutput which are not WorkflowStepInput
• red : WorkflowOutputParameter

Link with cwl-utils

Each node of the parsed networkx graph object has an attribute cwl_utils_object containing the cwl_utils object, among the following :

• WorkflowStep
• WorkflowStepInput
• WorkflowStepOutput
• WorkflowInputParameter
• WorkflowOutputParameter

The type of the node (one of the above in string) is accessible through the parameter node_type of each node.

License

Apache 2.0