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CWL Style Guide

This section outlines the BIXU Dev team style guide for cwl. It serves to standarize formatting to increase portability and understanding between team members.

CWL Style Guide

File format, with .cwl, should be in YAML format, when possible

Tool cwl

Field order and template:

cwlVersion: v1.0 # change if needed, but this is our default
class: CommandLine Tool
id: short_tool_name
doc: “Brief description of tool, can be expansive if a more complicated tool, like strelka2, annovar, etc” # doc strings should be double quoted
requirements:
  - class: ResourceRequirement
    ramMin: <int>
    coresMin: <int>
  - class: ClassRequirement
  - class: ClassRequirement2
baseCommand: [cmd1, arg1] # can be empty
arguments: # suggested
  - position: 0
    shellQuote: false
    valueFrom: >-
      cmd1/cmd1_arg1
      cmd1_arg2

      cmd2
      cmd2_arg1

inputs: #doc for inputs STRONGLY suggested, default optional
  in_var1_name: {type: string, doc: “describe input briefly”}
  in_var2_name: {type: int, doc: “describe input briefly”}
  in_var3_name: {type: 'File[]?', doc: “describe input briefly”} # recommend single quote complex file types
outputs:
  out_var1_name: 
    type: type
    outputBinding:
      glob: ‘<pattern>’
    doc: “Brief output description”
  out_var2_name: 
    type: type
    outputBinding:
      glob: ‘<pattern>’
    doc: “Brief output description”

Workflow cwl

Field order and template:

cwlVersion: v1.0 # change if needed, but this is our default
class: Workflow
id: short_wf_name
doc: “Brief description of workflow, can be expansive if a more complicated tool, like WGS align, RNAseq WF etc”
requirements:
  - class: ClassRequirement
  - class: ClassRequirement2

inputs: #doc for inputs STRONGLY suggested, default optional
  in_var1_name: {type: type, doc: “describe input briefly”}
  in_var2_name: {type: type, doc: “describe input briefly”} 

outputs:
  out_var1_name: {type: type, doc: “describe input briefly”,outputSource: <source>}
  out_var2_name: {type: type, doc: “describe input briefly”,outputSource: <source>}

steps:
  alias_for_tool:
    run: <relative_path_to_tool_cwl>
    in:
      tool_input_name1: <source>
      tool_input_name2: <source>
    scatter: <tool_input> # if applicable
    out: [output1, output2]

$namespaces: # if needed
  sbg: https://sevenbridges.com
hints: # if needed
  - class: 'sbg:maxNumberOfParallelInstances'
    value: 3