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Peter Amstutz
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Updating to draft-4.dev2
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‎draft-4/Process.yml

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- cwl:draft-3.dev5
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- cwl:draft-3
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- cwl:draft-4.dev1
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- cwl:draft-4.dev2
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- name: CWLType
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type: enum

‎draft-4/draft-4/binding-test.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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reference:

‎draft-4/draft-4/bwa-mem-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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class: CommandLineTool
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‎draft-4/draft-4/cat1-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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type: File
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inputBinding: {position: 1}
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numbering:
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type: ["null", boolean]
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type: boolean?
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inputBinding:
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position: 0
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prefix: -n

‎draft-4/draft-4/cat2-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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file1: File
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outputs: []
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baseCommand: cat
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stdin: $(inputs.file1.path)

‎draft-4/draft-4/cat3-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:

‎draft-4/draft-4/cat4-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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file1:
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type: File
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file1: File
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outputs:
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output_txt:
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type: File

‎draft-4/draft-4/cat5-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:

‎draft-4/draft-4/conflict-wf.cwl

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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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$graph:
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- id: echo
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class: CommandLineTool
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id: collision
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inputs:
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input_1:
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type: string
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input_2:
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type: string
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input_1: string
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input_2: string
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outputs:
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fileout:
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type: File
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source: "#collision/cat_step/fileout"
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outputSource: cat_step/fileout
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steps:
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echo_1:
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run: "#echo"
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in:
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text: "#collision/input_1"
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text: input_1
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out: [fileout]
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echo_2:
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run: "#echo"
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in:
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text: "#collision/input_2"
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text: input_2
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out: [fileout]
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cat_step:
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run: "#cat"
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in:
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file1:
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source: "#collision/echo_1/fileout"
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source: echo_1/fileout
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file2:
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source: "#collision/echo_2/fileout"
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source: echo_2/fileout
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out: [fileout]

‎draft-4/draft-4/count-lines1-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:
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outputs:
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count_output:
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type: int
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source: "#step2/output"
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source: step2/output
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steps:
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step1:

‎draft-4/draft-4/count-lines2-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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requirements:
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InlineJavascriptRequirement: {}
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‎draft-4/draft-4/count-lines3-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:

‎draft-4/draft-4/count-lines4-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:

‎draft-4/draft-4/count-lines5-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:

‎draft-4/draft-4/count-lines6-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:

‎draft-4/draft-4/count-lines7-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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requirements:
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- class: MultipleInputFeatureRequirement

‎draft-4/draft-4/count-lines8-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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file1:

‎draft-4/draft-4/count-lines9-wf.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs: []
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‎draft-4/draft-4/echo-tool.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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in:
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type: Any

‎draft-4/draft-4/env-tool1.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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in:
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type: string

‎draft-4/draft-4/env-tool2.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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in: string
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outputs:

‎draft-4/draft-4/env-wf1.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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in: string

‎draft-4/draft-4/env-wf2.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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in: string

‎draft-4/draft-4/formattest.cwl

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$namespaces:
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edam: "http://edamontology.org/"
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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class: CommandLineTool
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description: "Reverse each line using the `rev` command"
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inputs:

‎draft-4/draft-4/formattest2.cwl

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$schemas:
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- EDAM.owl
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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description: "Reverse each line using the `rev` command"
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inputs:

‎draft-4/draft-4/formattest3.cwl

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- EDAM.owl
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- gx_edam.ttl
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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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description: "Reverse each line using the `rev` command"
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inputs:

‎draft-4/draft-4/glob-expr-list.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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ids:

‎draft-4/draft-4/metadata.cwl

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- foaf.rdf
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- dcterms.rdf
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cwlVersion: cwl:draft-4.dev2
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class: CommandLineTool
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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‎draft-4/draft-4/null-expression1-tool.cwl

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class: ExpressionTool
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requirements:
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- class: InlineJavascriptRequirement
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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i1:

‎draft-4/draft-4/null-expression2-tool.cwl

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class: ExpressionTool
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requirements:
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- class: InlineJavascriptRequirement
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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i1:

‎draft-4/draft-4/optional-output.cwl

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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: "cwl:draft-4.dev1"
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cwlVersion: "cwl:draft-4.dev2"
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description: "Print the contents of a file to stdout using 'cat' running in a docker container."
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hints:
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DockerRequirement:

‎draft-4/draft-4/params.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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inputs:
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bar:
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type: Any

‎draft-4/draft-4/params2.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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requirements:
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- class: InlineJavascriptRequirement
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‎draft-4/draft-4/parseInt-tool.cwl

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class: ExpressionTool
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requirements:
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- class: InlineJavascriptRequirement
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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file1:

‎draft-4/draft-4/record-output.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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requirements:
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- class: ShellCommandRequirement
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inputs:

‎draft-4/draft-4/rename.cwl

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class: CommandLineTool
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cwlVersion: cwl:draft-4.dev1
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cwlVersion: cwl:draft-4.dev2
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baseCommand: "true"
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requirements:
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CreateFileRequirement:

‎draft-4/draft-4/revsort.cwl

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#
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class: Workflow
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description: "Reverse the lines in a document, then sort those lines."
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# Requirements & hints specify prerequisites and extensions to the workflow.
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# In this example, DockerRequirement specifies a default Docker container

‎draft-4/draft-4/revtool.cwl

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# Simplest example command line program wrapper for the Unix tool "rev".
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#
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class: CommandLineTool
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description: "Reverse each line using the `rev` command"
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# The "inputs" array defines the structure of the input object that describes

‎draft-4/draft-4/scatter-valuefrom-wf1.cwl

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#!/usr/bin/env cwl-runner
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class: Workflow
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inputs:
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inp:

‎draft-4/draft-4/scatter-valuefrom-wf2.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-4.dev1
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class: Workflow
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inputs:

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