2.18. Metadata and Authorship

Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. format: edam:format_2572) can use a namespace prefix listed in the $namespaces section of the document (e.g. edam: http://edamontology.org/) as described in the Schema Salad specification. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: format: http://edamontology.org/format_2572.

For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool.

metadata_example2.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool

label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

inputs:
  aligned_sequences:
    type: File
    label: Aligned sequences in BAM format
    format: edam:format_2572
    inputBinding:
      position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
  report:
    type: stdout
    format: edam:format_1964
    label: A text file that contains a line count

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-6130-1021
    s:email: mailto:dyuen@oicr.on.ca
    s:name: Denis Yuen

s:contributor:
  - class: s:Person
    s:identifier: http://orcid.org/0000-0002-7681-6415
    s:email: mailto:briandoconnor@gmail.com
    s:name: Brian O'Connor

s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2016-12-13"
s:license: https://spdx.org/licenses/Apache-2.0

$namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf
  - http://edamontology.org/EDAM_1.18.owl

The equivalent of this CWL description in command line format is:

$ wc -l /path/to/aligned_sequences.ext > output.txt

2.18.1. Extended Example

For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields.

metadata_example3.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool

label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

hints:
  ResourceRequirement:
    coresMin: 4

inputs:
  aligned_sequences:
    type: File
    label: Aligned sequences in BAM format
    format: edam:format_2572
    inputBinding:
      position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
  report:
    type: stdout
    format: edam:format_1964
    label: A text file that contains a line count

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-6130-1021
    s:email: mailto:dyuen@oicr.on.ca
    s:name: Denis Yuen

s:contributor:
  - class: s:Person
    s:identifier: http://orcid.org/0000-0002-7681-6415
    s:email: mailto:briandoconnor@gmail.com
    s:name: Brian O'Connor

s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2016-12-13"
s:license: https://spdx.org/licenses/Apache-2.0

s:keywords: edam:topic_0091 , edam:topic_0622
s:programmingLanguage: C

$namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/

$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf
  - http://edamontology.org/EDAM_1.18.owl