Defining jobs using CWL

CWL tools are defined using a YAML syntax. They specify the way in which a command is run.

When Jobarchitect uses CWL to run its jobs, it makes use of two hardcoded parameters, input_file and output_file. These are then dynamically generated from items in the dataset.

An example wrapping the cp command looks like this:

cwlVersion: v1.0
class: CommandLineTool
baseCommand: cp
inputs:
  input_file:
    type: File
    inputBinding:
      position: 1
  output_file:
    type: string
    inputBinding:
      position: 2
outputs:
   an_output_file:
     type: File
     outputBinding:
       glob: $(inputs.output_file)

This can then be combined with the job description file below.

input_file:
  class: File
  path: /Users/olssont/sandbox/cwl_v1/dummy.txt
output_file: dummycopy.txt

The job description files are generated dynamically by Jobarchitect’s agent (_analyse_by_ids) at runtime.

A different example using redirection (such that output is captured from stdout) is illustrated below:

cwlVersion: v1.0
class: CommandLineTool
inputs:
  input_file:
    type: File
    inputBinding: { position: 1 }
baseCommand: shasum
outputs:
  shasum: stdout
stdout: $(inputs.output_file)