.dockstore.yml

# Refers to the version 1.2 of the .dockstore.yml schema
version: 1.2

# An array of workflows.
workflows:

  # The optional workflow name for a workflow, which may only consist of alphanumerics
  # and internal underscores and hyphens, but no spaces or other characters. Names may not exceed 256 characters.
  # If using a .dockstore.yml with multiple workflows, this field is required
  # to uniquely identify workflows in the repository.
  #
  # It should be noted that having the name come first is an arbitrary decision.
  # You could use subclass instead, for instance. Provided arrays are not broken
  # up, the order of fields within a .dockstore.yml is not important.
  - name: CAMRA-Assembly_Quality_Control-WDL
  
    # The descriptor language used for the workflow. CWL, WDL, NFL (Nextflow), or GALAXY.
    # This cannot be changed once the workflow is registered.
    subclass: WDL

    # Workflow-wide setting that will affect ALL branches/tags; only set this as needed in a main branch.
    # Set to true to publish an unpublished workflow, or false to unpublish a published workflow.
    # Omitting the publish setting leaves the publish-state unchanged (recommended for all non-primary branches).
    # publish: <Boolean>
  
    # The absolute path to the primary descriptor file in the Git repository.
    # - For CWL, the primary descriptor is a .cwl file.
    # - For WDL, the primary descriptor is a .wdl file.
    # - For Galaxy, the primary descriptor is a .ga file.
    # - Nextflow differs from these as the primary descriptor is a nextflow.config file.
    primaryDescriptorPath: /Workflows/CAMRA_QC_WF.wdl

    # An optional path to a workflow-specific readme in the Git repository. If not provided, Dockstore will show
    # the readme.md present at the root of the Git repository if it is present.
    # If you have multiple workflows in a single Git repository, it is recommend to give each one a readme.
    readMePath: /README.md

    # A boolean that will change the default version to be displayed on Dockstore. Default: False.
    # A value of true will automatically display the latest tag updated as default.
    # A value of false will retain the default version that has been specified via the Dockstore UI.
    latestTagAsDefault: True
    
    # An optional array of authorship information.
    # Note that if orcid is present, then all other fields will be ignored, as information will be taken from orcid.
    # If orcid is not present, make sure to at a minimum include the name field for each author.
    authors:
      - orcid: 0009-0008-5199-2990 # Daniella Matute
      - name: Andrew LaPointe
        email: andrewrlapointe@gmail.com

    # An optional array of absolute paths to test parameter files in the Git repository.
    # For example...
    # testParameterFiles:
    #   - /null-model/null-model.json
    #   - /null-model/null-model-binary.json
    # testParameterFiles: <String Array>

    # The optional filters section allow specifying sets of Git branches and tags to include for the workflow.
    # If no filters are given, all branches and tags are included.
    # Branches and tags are arrays of pattern-strings.
    # Pattern-strings use Unix-style Glob syntax by default (Ex: `develop`, `myworkflow/**`)
    # https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/FileSystem.html#getPathMatcher(java.lang.String)
    # or RegEx when the string is surrounded by / (Ex: `/develop/`, `/myworkflow\/.*/`).
    # filters:
    #   branches: [ /.*dockstore/ ]
    #   tags: [ /v.*dockstore/ ]
    branches:
      - main 

    
  - name: CAMRA-Genome_Assembly-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_ASM_WF.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
      - name: Andrew LaPointe
        email: andrewrlapointe@gmail.com
        
  - name: CAMRA-Genome_Annotation-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_ANNOT_WF.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
      - name: Andrew LaPointe
        email: andrewrlapointe@gmail.com
        
  - name: CAMRA-AMR_Detection-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_WF.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main 
      - term_consolidation

  - name: RGI-BLASTN
    subclass: WDL
    primaryDescriptorPath: /Workflows/sub_wdl/rgi.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - RGI

  - name: CAMRA-NIGERIA_AMR_Detection-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_WF_NIGERIA.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
 
  - name: CAMRA-CAMRA-BV-BRC-AMR-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA-BV-BRC-AMR.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-BV-BRC-AMR-NO-ASSEM-WDL
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA-BV-BRC-AMR-NO-ASM.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-AMR-ABRICATE
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_ABRICATE.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
      
  - name: CAMRA-AMR-AMRFINDER
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_AMRFINDER.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
 
  - name: CAMRA-AMR-RESFINDER
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_RESFINDER.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-AMR-RGI
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_RGI.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-AMR-HARMONIZATION
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_AMR_HARMONIZATION_WF.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-MAKE_ORGANISM
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_Make_Organism.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
 
  - name: CAMRA-GET-MLST
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_MLST_WF.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-PANGENOME
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_RUN_PANGENOME.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main

  - name: CAMRA-PANBLAST
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_PAN_BLAST.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
      
  - name: CAMRA-MOB-SUITE
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_MOB_SUITE.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main
 
  - name: CAMRA-GEOMAPPER
    subclass: WDL
    primaryDescriptorPath: /Workflows/CAMRA_GEOMAPPER.wdl
    readMePath: /README.md
    latestTagAsDefault: True
    authors:
      - orcid: 0009-0008-5199-2990 #Daniella Matute
    branches:
      - main