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Peter Amstutz
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Merge commit '4cadc611dfced4e1a818e6afbb215270fc2561b3' into draft-4
2 parents 668e6ca + 4cadc61 commit f1901b9

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‎cwltool/schemas/draft-4/CommandLineTool.yml

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@@ -244,7 +244,7 @@ $graph:
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the File objects must include up to the first 64 KiB of file contents
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in the `contents` field.
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- name: InitialWorkingDirectory
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- name: initialWorkDir
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type: record
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doc: |
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Setup a working directory based on a number of input files (and/or directories)
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type: "array"
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items: "#EnvironmentDef"
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doc: The list of environment variables.
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jsonldPredicate:
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mapSubject: envName
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mapPredicate: envValue
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- type: record

‎cwltool/schemas/draft-4/Process.yml

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@@ -520,9 +520,6 @@ $graph:
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- "null"
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- type: array
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items: Any
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jsonldPredicate:
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_id: "cwl:hints"
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mapSubject: class
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doc: |
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Declares hints applying to either the runtime environment or the
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workflow engine that may be helpful in executing this process. It is
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jsonldPredicate:
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_id: cwl:hints
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noLinkCheck: true
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mapSubject: class
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- name: label
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type:
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- "null"

‎cwltool/schemas/draft-4/Workflow.yml

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@@ -324,15 +324,13 @@ $graph:
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items: "Any"
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jsonldPredicate:
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_id: "cwl:hints"
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noLinkCheck: true
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mapSubject: class
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doc: |
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Declares hints applying to either the runtime environment or the
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workflow engine that may be helpful in executing this workflow step. It is
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not an error if an implementation cannot satisfy all hints, however
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the implementation may report a warning.
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jsonldPredicate:
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_id: cwl:hints
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noLinkCheck: true
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- name: label
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type:
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- "null"
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type:
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- type: array
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items: "#WorkflowStep"
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jsonldPredicate:
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mapSubject: id
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- type: record

‎cwltool/schemas/draft-4/draft-4/binding-test.cwl

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@@ -1,14 +1,14 @@
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#!/usr/bin/env cwl-runner
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class: CommandLineTool
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cwlVersion: cwl:draft-3
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cwlVersion: cwl:draft-4.dev1
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inputs:
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- id: reference
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reference:
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type: File
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inputBinding: { position: 2 }
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- id: reads
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reads:
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type:
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type: array
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items: File

‎cwltool/schemas/draft-4/draft-4/bwa-mem-tool.cwl

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@@ -1,41 +1,41 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-3
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cwlVersion: cwl:draft-4.dev1
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class: CommandLineTool
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hints:
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- class: DockerRequirement
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DockerRequirement:
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dockerPull: images.sbgenomics.com/rabix/bwa
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dockerImageId: 9d3b9b0359cf
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- class: ResourceRequirement
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ResourceRequirement:
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coresMin: 4
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inputs:
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- id: reference
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reference:
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type: File
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inputBinding: { position: 2 }
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- id: reads
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reads:
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type:
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type: array
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items: File
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inputBinding: { position: 3 }
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- id: minimum_seed_length
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minimum_seed_length:
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type: int
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inputBinding: { position: 1, prefix: -m }
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- id: min_std_max_min
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min_std_max_min:
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type: { type: array, items: int }
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inputBinding:
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position: 1
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prefix: -I
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itemSeparator: ","
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outputs:
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- id: sam
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sam:
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type: File
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outputBinding: { glob: output.sam }
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‎cwltool/schemas/draft-4/draft-4/cat1-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-3
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cwlVersion: cwl:draft-4.dev1
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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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- class: DockerRequirement
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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- id: file1
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file1:
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type: File
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inputBinding: {position: 1}
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- id: numbering
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numbering:
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type: ["null", boolean]
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inputBinding:
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position: 0

‎cwltool/schemas/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-3
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cwlVersion: cwl:draft-4.dev1
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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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- class: DockerRequirement
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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- id: file1
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file1:
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type: File
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outputs: []
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baseCommand: cat

‎cwltool/schemas/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-3
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cwlVersion: cwl:draft-4.dev1
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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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- class: DockerRequirement
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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- id: file1
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file1:
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type: File
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label: Input File
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description: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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- id: output_file
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output_file:
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type: File
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outputBinding: {glob: output.txt}
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baseCommand: cat

‎cwltool/schemas/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-3
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cwlVersion: cwl:draft-4.dev1
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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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- class: DockerRequirement
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DockerRequirement:
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dockerPull: debian:wheezy
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inputs:
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- id: file1
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file1:
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type: File
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outputs:
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- id: output_txt
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output_txt:
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type: File
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outputBinding:
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glob: output.txt

‎cwltool/schemas/draft-4/draft-4/cat5-tool.cwl

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#!/usr/bin/env cwl-runner
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cwlVersion: cwl:draft-3
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cwlVersion: cwl:draft-4.dev1
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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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- class: DockerRequirement
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DockerRequirement:
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dockerPull: "debian:wheezy"
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- class: BlibberBlubberFakeRequirement
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BlibberBlubberFakeRequirement:
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fakeField: fraggleFroogle
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inputs:
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- id: file1
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file1:
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type: File
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label: "Input File"
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description: "The file that will be copied using 'cat'"
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inputBinding: {position: 1}
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outputs:
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- id: output_file
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output_file:
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type: File
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outputBinding: {glob: output.txt}
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baseCommand: cat

‎cwltool/schemas/draft-4/draft-4/conflict-wf.cwl

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cwlVersion: cwl:draft-3
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cwlVersion: cwl:draft-4.dev1
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$graph:
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- class: CommandLineTool
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id: echo
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- id: echo
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class: CommandLineTool
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inputs:
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- id: text
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text:
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type: string
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inputBinding: {}
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outputs:
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- id: fileout
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fileout:
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type: File
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outputBinding:
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glob: out.txt
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baseCommand: echo
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stdout: out.txt
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- class: CommandLineTool
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id: cat
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- id: cat
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class: CommandLineTool
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inputs:
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- id: file1
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file1:
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type: File
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inputBinding:
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position: 1
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- id: file2
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file2:
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type: File
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inputBinding:
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position: 2
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outputs:
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- id: fileout
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fileout:
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type: File
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outputBinding:
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glob: out.txt
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id: collision
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inputs:
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- id: input_1
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input_1:
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type: string
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- id: input_2
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input_2:
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type: string
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outputs:
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- id: fileout
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fileout:
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type: File
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source: "#collision/cat_step/fileout"
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steps:
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- id: echo_1
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echo_1:
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run: "#echo"
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inputs:
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- id: text
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source: "#collision/input_1"
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outputs:
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- id: fileout
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in:
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text: "#collision/input_1"
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out: [fileout]
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- id: echo_2
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echo_2:
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run: "#echo"
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inputs:
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- id: text
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source: "#collision/input_2"
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outputs:
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- id: fileout
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in:
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text: "#collision/input_2"
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out: [fileout]
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- id: cat_step
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cat_step:
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run: "#cat"
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inputs:
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- id: file1
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in:
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file1:
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source: "#collision/echo_1/fileout"
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- id: file2
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file2:
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source: "#collision/echo_2/fileout"
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outputs:
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- id: fileout
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out: [fileout]

‎cwltool/schemas/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-3
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cwlVersion: cwl:draft-4.dev1
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inputs:
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- { id: file1, type: File }
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file1:
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type: File
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outputs:
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- id: count_output
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count_output:
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type: int
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source: "#step2/output"
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steps:
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- id: step1
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step1:
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run: wc-tool.cwl
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inputs:
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- {id: file1, source: "#file1"}
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outputs:
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- {id: output}
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in:
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file1: "#file1"
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out: [output]
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- id: step2
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step2:
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run: parseInt-tool.cwl
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inputs:
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- {id: file1, source: "#step1/output"}
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outputs:
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- {id: output}
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in:
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file1: "#step1/output"
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out: [output]

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