Example cwl workflow (for v1.0)?

Question

[Peter vH]

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?

Answer 1

[Michael R. Crusoe]

Hello Peter vH!

For workflows we have "in" and "out". CommandLineTools use 'inputs' and 'outputs'. You've mixed the two in your workflow and the last line of the overly detailed error message says as much. Our apologies for the error messages being so hard to read.

[aebmad]

Hi Michael, I'm looking into upgrading the workflows that we have at Duke-GCB from version draft3 to 1.0. Is there any document that specifies the differences introduced by v1.0? I can't find it. Thanks!

[alaindomissy]

Changes from draft-3 to version 1.0 are listed in paragraph 1.1 on this page: http://www.commonwl.org/v1.0/CommandLineTool.html#Introduction_to_v1.0

There is also a preliminary tool to convert cwl tools (not workflows yet) from draft-3 to v1.0 here : https://github.com/common-workflow-language/cwl-upgrader