I'm trying to write a CWL workflow that will do a simple trim and map procedure on some bacterial short read data that I've got. For the trimming I'm planning on using trimmomatic and I have modified the Duke-GCB trimmomatic tool slightly for this purpose (see https://github.com/pvanheus/GGR-cwl/blob/master/trimmomatic/trimmomatic.cwl). Here is the CWL for the workflow (trim.cwl):

cwlVersion: v1.0
class: Workflow
inputs: 
  reads1: File
  reads2: File
  slidingw: string
  minl: string
outputs:
  trimmed_reads:
    type: File
    outputSource: trim_reads/output_read1_trimmed_file

steps:
  trim_reads:
    run: { $import: "../../tools/trimmomatic/trimmomatic.cwl" }
    inputs:
      input_read1_fastq_file: reads1
      input_read2_fastq_file: reads2
      slidingwindow: slidingw
      minlen: minl
    out: [output_read1_trimmed_file]

but trying to run this with cwltool trim.cwl yields:

cwltool 1.0.20160714182449
Tool definition failed validation:
Validation error in object file:///net/ceph-mon1.sanbi.ac.za/sanbi/scratch/pvh/cwl/workflows/trim/trim.cwl
  Could not validate as `CommandLineTool` because
    could not validate field `outputs` because
      At position 0
        could not validate field `outputSource` because it is not recognized and strict is True, valid fields are: label, secondaryFiles, format, streamable, doc, id, outputBinding, type

    missing required field `baseCommand`
    could not validate field `steps` because it is not recognized and strict is True, valid fields are: id, inputs, outputs, requirements, hints, label, doc, cwlVersion, class, baseCommand, arguments, stdin, stderr, stdout, successCodes, temporaryFailCodes, permanentFailCodes
  Could not validate as `ExpressionTool` because
    could not validate field `outputs` because
      At position 0
        could not validate field `outputSource` because it is not recognized and strict is True, valid fields are: label, secondaryFiles, format, streamable, doc, id, outputBinding, type

    missing required field `expression`
    could not validate field `steps` because it is not recognized and strict is True, valid fields are: id, inputs, outputs, requirements, hints, label, doc, cwlVersion, class, expression
  Could not validate as `Workflow` because
    could not validate field `steps` because
      the value `[{'id': 'file:///net/ceph-mon1.sanbi.ac.za/sanbi/scratch/pvh/cwl/workflows/trim/trim.cwl#trim_reads'
        'inputs': [{'id': u'file:///net/ceph-mon1.sanbi.ac.za/sa[...]`
       is not a valid type in the union, expected one of:
      - array of <WorkflowStep>, but
         At position 0
          missing required field `in`
          could not validate field `inputs` because it is not recognized and strict is True, valid fields are: id, in, out, requirements, hints, label, doc, run, scatter, scatterMethod

I'm sure there are all sorts of errors in my CWL, but the parsing as a CommandLineTool is surely the wrong thing?