Workflow creation

Workflows are a key part of SciWIn as they are even part of the name (Scientific Workflow Infrastructure). SciWin Client facilitates the creation of CWL workflows from exisiting CWL CommandLineTools. Workflows in s4n are created piece by piece using a command for each edge of the directed acyclic graph (DAG) that represents the workflow.

Creating a blank workflow

A blank workflow file can be created by using the s4n workflow create command.

Command

s4n workflow create my-workflow

my-workflow.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow

inputs: []
outputs: []
steps: []

Creating connections

Connections can be seen as the arrows in the above figure. Think about a sentence like

The arrow points from the input slot called speakers to the calculation steps input.

Therefore the command that created this arrow was s4n workflow connect my-workflow --from @inputs/speakers --to calculation/speakers.

In this simple example we will connect the echo command with the cat command. Use the following Commands to create the needed command line tool specifications.

Command

s4n tool create echo "Hello World" \> greeting.txt
s4n tool create cat greeting.txt
s4n workflow create echo-cat

To get an overview of the available slots the s4n tool ls -a command can be used.

+------+------------------+---------------+
| Tool | Inputs           | Outputs       |
+------+------------------+---------------+
| echo | echo/hello_world | echo/greeting |
+------+------------------+---------------+
| cat  | cat/greeting_txt |               |
+------+------------------+---------------+

As input parameter we wish to use the hello-world input of the echo tool and connect the output echo/greeting to the input cat/greeting_txt. Therefore 3 connections are needed.

Connecting a new input to echo step

Command

s4n workflow connect echo-cat --from @inputs/message --to echo/hello_world

echo-cat.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow

inputs:
- id: message
  type: string

outputs: []
steps:
- id: echo
  in:
    hello_world: message
  run: '../echo/echo.cwl'
  out:
  - greeting

Connecting the output of the echo step to the cat step

Command

s4n workflow connect echo-cat --from echo/greeting --to cat/greeting_txt

echo-cat.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: Workflow

inputs:
- id: message
  type: string

outputs: []
steps:
- id: echo
  in:
    hello_world: message
  run: '../echo/echo.cwl'
  out:
  - greeting
- id: cat
  in:
    greeting_txt: echo/greeting
  run: '../cat/cat.cwl'
  out: []

To save the workflow s4n workflow save echo-cat is used.

Workflow visualizations can be achieved using s4n workflow visualize

s4n workflow visualize -r dot workflows/echo-cat/echo-cat.cwl | dot -Tsvg > workflow.svg