BashCommand step

Cloudgene supports the execution of executable binaries.

Parameters

Parameter	Required	Description
type	yes	Type has to be command
cmd	yes	The command that should be executed
bash	no	Enables or disable Bash specific features like pipes and loops (default: false)
stdout	no	Use stdout as step's output (default: false)

Examples

Print message to using /bin/echo

This example shows how to forward stdout directly to the output of a step in order to display it the web-application.

id: cmd-example
name: Command Example
version: 1.0
workflow:
  steps:
    - name: Print text to terminal
      type: command
      cmd: /bin/echo $message
      stdout: true
  inputs:
    - id: message
      description: Message
      type: text

Write message to a file using stdout streaming

This example shows how to use Bash specific features by setting the bash property to true:

id: bash-example
name: Bash Example
version: 1.0
workflow:
  steps:
    - name: Write text to file using pipes
      type: command
      cmd: /bin/echo $message > $output
      bash: true
  inputs:
    - id: message
      description: Message
      type: text
  outputs:
    - id: output
      description: Output File
      type: local_file