Example workflow definitions

version 1.1

task my_task {
   runtime { ... }
   inputs {
       File input_file
       String name
       Int threshold
   }
   
   command <<<
   my_tool --name ~{name} --threshold ~{threshold} ~{input_file}
   >>>
   
   output {
       File results = "results.txt"
   }
}

workflow my_workflow {
   inputs {
       File input_file
       String name
       Int threshold = 50
   }
   
   call my_task {
       input:
          input_file = input_file,
          name = name,
          threshold = threshold
   }
   outputs {
       File results = my_task.results
   }
}           

nextflow.enable.dsl = 2

params.input_file = null
params.name = null
params.threshold = 50

process my_task {
   // <directives>
   
   input:
     path input_file
     val name
     val threshold
   
   output:
     path 'results.txt', emit: results
   
   script:
     """
     my_tool --name ${name} --threshold ${threshold} ${input_file}
     """
     
   
}

workflow MY_WORKFLOW {
   my_task(
       params.input_file,
       params.name,
       params.threshold
   )
}

workflow {
   MY_WORKFLOW()
}
              
            

cwlVersion: v1.2
class: Workflow

requirements:
    InlineJavascriptRequirement: {}

inputs:
   input_file: File
   name: string
   threshold: int

outputs:
    result:
        type: ...
        outputSource: ...

steps:
    my_task:
        run:
            class: CommandLineTool
            baseCommand: my_tool
            requirements:
                ...
            inputs:
                name:
                    type: string
                    inputBinding:
                        prefix: "--name"
                threshold:
                    type: int
                    inputBinding:
                        prefix: "--threshold"
                input_file:
                    type: File
                    inputBinding: {}
            outputs:
                results:
                    type: File
                    outputBinding:
                        glob: results.txt