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Merge pull request #1 from dockstore-testing/feature/grab_bag
Feature/grab bag
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‎.dockstore.yml‎

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version: 1.2
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tools:
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- subclass: CWL
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primaryDescriptorPath: /md5sum/dockstore-tool-md5sum.cwl
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testParameterFiles:
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- /md5sum/md5sum.json
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name: cwl_tool
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authors:
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- orcid: 0000-0002-6130-1021
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workflows:
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- subclass: CWL
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primaryDescriptorPath: /md5sum/md5sum.cwl
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testParameterFiles:
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- /md5sum/md5sum.json
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name: cwl_workflow
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authors:
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- orcid: 0000-0002-6130-1021
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- subclass: WDL
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primaryDescriptorPath: /md5sum/md5sum.wdl
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testParameterFiles:
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- /md5sum/md5sum.wdl.json
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name: wdl
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authors:
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- orcid: 0000-0002-6130-1021

‎.github/workflows/validate.yml‎

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name: Validate workflows
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on: [push]
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jobs:
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build:
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Setup engines
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run: |
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curl -o requirements.txt "https://raw.githubusercontent.com/dockstore/dockstore/1.13.0-beta.3/dockstore-webservice/src/main/resources/requirements/1.13.0/requirements3.txt"
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pip3 install --user -r requirements.txt
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- run: sudo apt-get install -y moreutils
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- name: Validate cwl
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run: |
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cwltool --validate checker_workflow_wrapping_tool.cwl
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cwltool --validate checker_workflow_wrapping_workflow.cwl
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- name: Validate wdl
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run: |
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wget https://github.com/broadinstitute/cromwell/releases/download/83/womtool-83.jar
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java -jar womtool-83.jar validate checker.wdl

‎.github/workflows/workflows.yml‎

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name: Test workflows
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on: [push]
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jobs:
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build:
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runs-on: ubuntu-22.04
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.9'
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- name: Setup engines
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run: |
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curl -o requirements.txt "https://raw.githubusercontent.com/dockstore/dockstore/1.13.0-beta.3/dockstore-webservice/src/main/resources/requirements/1.13.0/requirements3.txt"
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pip3 install --user -r requirements.txt
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- name: Setup CLI
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run: |
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curl -L -o dockstore https://github.com/dockstore/dockstore/releases/download/1.12.2/dockstore
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chmod +x dockstore
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mkdir /home/runner/dockstore_bin
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mv dockstore /home/runner/dockstore_bin
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echo "/home/runner/dockstore_bin" >> $GITHUB_PATH
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- name: Prime CLI
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run: |
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echo "$PATH"
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mkdir ~/.dockstore
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# we recommend suppressing INFO output for Cromwell, but if you run into a problem
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# you may need to change ERROR to INFO to give you hints on how to debug
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printf "cromwell-vm-options: -DLOG_LEVEL=ERROR\nserver-url: https://dockstore.org/api" > ~/.dockstore/config
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dockstore
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- name: Run cwl workflows with CLI
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run: |
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dockstore --script workflow launch --local-entry checker_workflow_wrapping_workflow.cwl --json md5sum.json
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dockstore --script workflow launch --local-entry checker_workflow_wrapping_tool.cwl --json md5sum.json
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- name: Run wdl workflow with CLI
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run: |
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dockstore --script workflow launch --local-entry checker.wdl --json md5sum.wdl.json

‎README.md‎

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```
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java -jar ~/.dockstore/libraries/cromwell-29.jar run --inputs md5sum.wdl.json checker.wdl
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```
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## With Dockstore CLI
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If the Dockstore CLI is setup, the github actions setup in this repo demonstrate how to run these workflows with it.

‎checker_workflow_wrapping_tool.cwl‎

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cwlVersion: v1.0
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class: Workflow
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dct:creator:
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'@id': http://orcid.org/0000-0002-7681-6415
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foaf:name: Brian O'Connor
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foaf:mbox: mailto:briandoconnor@gmail.com
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s:author:
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- class: s:Person
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s:identifier: http://orcid.org/0000-0002-7681-6415
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s:email: mailto:briandoconnor@gmail.com
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s:name: Brian O'Connor
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dct:contributor:
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foaf:name: Denis Yuen
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foaf:mbox: mailto:denis.yuen@oicr.on.ca
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s:contributor:
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- class: s:Person
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s:identifier: https://orcid.org/0000-0002-6130-1021
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s:email: mailto:dyuen@oicr.on.ca
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s:name: Denis Yuen
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inputs:
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input_file: File
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doc: |
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This demonstrates how to wrap a "real" tool with a checker workflow that runs both the tool and a tool that performs verification of results
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$namespaces:
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s: https://schema.org/
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edam: http://edamontology.org/
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$schemas:
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- https://schema.org/version/latest/schemaorg-current-http.rdf
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- http://edamontology.org/EDAM_1.18.owl

‎checker_workflow_wrapping_workflow.cwl‎

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cwlVersion: v1.0
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class: Workflow
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dct:creator:
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'@id': http://orcid.org/0000-0002-7681-6415
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foaf:name: Brian O'Connor
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foaf:mbox: mailto:briandoconnor@gmail.com
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s:author:
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- class: s:Person
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s:identifier: http://orcid.org/0000-0002-7681-6415
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s:email: mailto:briandoconnor@gmail.com
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s:name: Brian O'Connor
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dct:contributor:
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foaf:name: Denis Yuen
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foaf:mbox: mailto:denis.yuen@oicr.on.ca
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s:contributor:
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- class: s:Person
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s:identifier: https://orcid.org/0000-0002-6130-1021
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s:email: mailto:dyuen@oicr.on.ca
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s:name: Denis Yuen
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requirements:
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- class: SubworkflowFeatureRequirement
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doc: |
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This demonstrates how to wrap a "real" workflow with a checker workflow that runs both the tool and a tool that performs verification of results
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$namespaces:
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s: https://schema.org/
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edam: http://edamontology.org/
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$schemas:
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- https://schema.org/version/latest/schemaorg-current-http.rdf
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- http://edamontology.org/EDAM_1.18.owl

‎md5sum/dockstore-tool-md5sum.cwl‎

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cwlVersion: v1.0
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$namespaces:
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dct: http://purl.org/dc/terms/
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foaf: http://xmlns.com/foaf/0.1/
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s: https://schema.org/
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edam: http://edamontology.org/
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doc: |
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[![Docker Repository on Quay.io](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum/status "Docker Repository on Quay.io")](https://quay.io/repository/briandoconnor/dockstore-tool-md5sum)
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[![Build Status](https://travis-ci.org/briandoconnor/dockstore-tool-md5sum.svg)](https://travis-ci.org/briandoconnor/dockstore-tool-md5sum)
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A very, very simple Docker container for the md5sum command. See the [README](https://github.com/briandoconnor/dockstore-tool-md5sum/blob/master/README.md) for more information.
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#dct:creator:
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# '@id': http://orcid.org/0000-0002-7681-6415
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# foaf:name: Brian O'Connor
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# foaf:mbox: briandoconnor@gmail.com
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requirements:
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- class: DockerRequirement
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dockerPull: quay.io/briandoconnor/dockstore-tool-md5sum:1.0.4

‎md5sum/md5sum.cwl‎

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cwlVersion: v1.0
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class: Workflow
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dct:creator:
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'@id': http://orcid.org/0000-0002-7681-6415
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foaf:name: Brian O'Connor
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foaf:mbox: mailto:briandoconnor@gmail.com
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dct:contributor:
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foaf:name: Denis Yuen
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foaf:mbox: mailto:denis.yuen@oicr.on.ca
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s:contributor:
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- class: s:Person
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s:identifier: https://orcid.org/0000-0002-6130-1021
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s:email: mailto:dyuen@oicr.on.ca
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s:name: Denis Yuen
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s:author:
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- class: s:Person
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s:identifier: http://orcid.org/0000-0002-7681-6415
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s:email: mailto:briandoconnor@gmail.com
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s:name: Brian O'Connor
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inputs:
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input_file: File
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in:
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input_file: input_file
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out: [output_file]
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$namespaces:
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s: https://schema.org/
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edam: http://edamontology.org/
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$schemas:
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- https://schema.org/version/latest/schemaorg-current-http.rdf
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- http://edamontology.org/EDAM_1.18.owl

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