connect/disconnect

connect and disconnect

The connect and disconnect commands can be used to connect CWL CommandLineTools, workflow inputs and workflow outputs forming a directed acyclic graph. The connect command establishes a connection and adds in-, outputs and steps if they are not present in the current workflow. The names of the steps slots can be copied from the output of s4n list. For connections to in- or outputs a @ has to be used es prefix e.g. @inputs/my-file. The name of the node is constructed by using the tool’s name and the name of the tool’s node separated by a forward slash: mytool/my-input. Connections are made using the --from and --to arguments together with the name of the workflow. If the Workflow does not exist when creating the first connection, the workflow will be created automatically.

Usage

Connects a workflow node

Usage: s4n connect --from <FROM> --to <TO> <NAME>

Arguments:
  <NAME>  Name of the workflow name to be altered

Options:
  -f, --from <FROM>  Starting Node: [tool]/[output]
  -t, --to <TO>      Ending Node: [tool]/[input]
  -h, --help         Print help

Example: Connect to input socket

s4n connect my-workflow --from @inputs/population --to calculation/population

Will add a new input socket population and adds the calculation step if it is not present in the workflow already. The step’s input population will be mapped to the workflow’s input.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow

inputs:
- id: population
  type: File

outputs: []
steps:
- id: calculation
  in:
    population: population
  run: '../calculation/calculation.cwl'
  out:
  - results

Connecting to workflow outputs works analogues.

Example: Connecting Tools

s4n connect my-workflow --from calculation/results --to plot/results

Will add a connection between two CWL CommandLineTools mapping the results output of the calculation tool to the results input of the plot tool.

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow

inputs: []
outputs: []
steps:
- id: calculation
  in: {}
  run: '../calculation/calculation.cwl'
  out:
  - results
- id: plot
  in:
    results: calculation/results
  run: '../plot/plot.cwl'
  out:
  - results

The same logic applies for the disconnect command.

Usage

Disconnects a workflow node

Usage: s4n disconnect --from <FROM> --to <TO> <NAME>

Arguments:
  <NAME>  Name of the workflow name to be altered

Options:
  -f, --from <FROM>  Starting Node: [tool]/[output]
  -t, --to <TO>      Ending Node: [tool]/[input]
  -h, --help         Print help