first try

[lindenb]

Hi Peter, thank your for your help.

My current interest is to translate my Makefile-based workflows to other engines. So my first idea is to just implement a minimal workflow, something like:

.PHONY: all
all: hello.txt
hello.txt:
    echo "Hello" > hello.txt

• There is no input to my workflow (should I always specify a json ? does the name of the json matters ? is a dot in an 'id' means it's a key of a json object ?)
• There is "no" declared output (how to specify 'constant' Files ?)

my attempt so far:

#!/usr/bin/env cwl-runner

- id: "#echocmd"
  class: CommandLineTool
  inputs:
    - id: "#echo-in"
      type: string
      label: "Message"
      description: "The message to print"
      default: "Hello World"
  outputs:
    - id: "#echo-out"
      type: File
      label: "Printed Message"
      description: "The file containing the message"
      outputBinding:
        glob: messageout.txt
  baseCommand: echo
  stdout: messageout.txt

- id: "#main"
  class: Workflow
  label: "Hello World"
  description: "Puts a message into a file using echo"
  inputs: []
  outputs:
    - id: "#main.output"
      type: File
      source: "#param.output"
  steps :
    - id: "#step0"
      run: {import: "#echocmd"}
      inputs: []
      outputs:
        - { id: "#main.output" }

(well I tried a few variations of this, without success...) The specification is quite large, and honestly, I didn't read/understand the whole document.

How can I make it run please ? :-)

Of course, don't accept this pull request for now. :-)

While I'm here:

• can I specify a whole bash line in a CommandLineTool ? something like :

   shell: /bin/bash
    baseCommand: " echo \"A'\  | tr 'A' B' | grep B "

Thank you for your help,

Pierre

[tetron]

You are pretty close, just a few changes:

• You need to put inputBinding: {} on the #echo-in parameter to indicate you want it added to the command line.
• The output parameter of #step0 should be named #step0.echo-out (this is formed from the id of the step and name of the output parameter).
• Correspondingly the workflow output should be connected to the step output with source: #step0.echo-out

Here's the fixed up version:

#!/usr/bin/env cwl-runner

- id: "#echocmd"
  class: CommandLineTool
  inputs:
    - id: "#echo-in"
      type: string
      label: "Message"
      description: "The message to print"
      default: "Hello World"
      inputBinding: {}
  outputs:
    - id: "#echo-out"
      type: File
      label: "Printed Message"
      description: "The file containing the message"
      outputBinding:
        glob: messageout.txt
  baseCommand: echo
  stdout: messageout.txt

- id: "#main"
  class: Workflow
  label: "Hello World"
  description: "Puts a message into a file using echo"
  inputs: []
  outputs:
    - id: "#main.output"
      type: File
      source: "#echocmd.echo-out"
  steps :
    - id: "#step0"
      run: {import: "#echocmd"}
      inputs: []
      outputs:
        - { id: "#echocmd.echo-out" }

[lindenb]

:+1: thanks; I'll update the code on monday

[lindenb]

OK, I've updated my cwl, It's working now , thanks ! :-)

[lindenb]

10H23: added a second example hello-param.cwl with parameters.

[mr-c]

I like this. @lindenb do you mind if I merge it in?

[lindenb]

@mr-c yes, you can merge :-)

I've got some other questions/test-cases. I'll ask for help in another pull-request.

Thanks

[mr-c]

My pleasure!