sync.yml

# Candace Savonen Jan 2025
# For info on how to update this file see: https://github.com/marketplace/actions/repo-file-sync-action#%EF%B8%8F-sync-configuration

group:
  - files:
      - source: .github/workflows/
        dest: .github/workflows/
        deleteOrphaned: true
        exclude: |
          transfer-rendered-files.yml
          send-updates.yml
          test-send-updates.yml
          starting-course.yml
          release-notes.yml
          docker-test.yml
          docker-build.yml
      - source: scripts/
        dest: scripts/
        deleteOrphaned: true
      - source: assets/box_images/
        dest: assets/box_images/
      - source: resources/exclude_files.txt
        dest: resources/exclude_files.txt
      - source: config_automation.yml
        dest: config_automation.yml
  # Repositories to receive changes
    repos: |
      jhudsl/Documentation_and_Usability
      jhudsl/Informatics_Research_Leadership
      jhudsl/Data_Management_for_Cancer_Research
      jhudsl/Computing_for_Cancer_Informatics
      jhudsl/Adv_Reproducibility_in_Cancer_Informatics
      jhudsl/Reproducibility_in_Cancer_Informatics
      jhudsl/Dissemination_and_Engagement
      fhdsl/Cancer_Clinical_Informatics
      jhudsl/Machine_Learning_for_Cancer_Informatics
      jhudsl/Cancer_Informatics_Data_Visualization
      jhudsl/Cancer_Genome_Informatics
      fhdsl/Cancer_Imaging_Informatics
      datatrail-jhu/DataTrail_Template
      abyzovlab/CNVpytor-course
      tmm211/dsp-terra-mooc-test2
      fhdsl/Choosing_Genomics_Tools
      fhdsl/NIH_Data_Sharing
      fhdsl/FH_Cluster_Guide
      fhdsl/Using_Leanpub
      fhdsl/Ethical_Data_Handling_for_Cancer_Research
      fhdsl/Overleaf_and_LaTeX_for_Scientific_Articles
      fhdsl/Design_of_Data_Analysis
      fhdsl/Tools_for_Reproducible_Workflows_in_R
      fhdsl/Introduction_to_reproducible_research
      mccoy-lab/hgv_modules
      griffithlab/pVACtools_Intro_Course
      griffithlab/CIVIC_SVI_Course
      PracticalGenomics/cogaps-on-sciserver
      fhdsl/AI_for_Efficient_Programming
      fhdsl/AI_for_Decision_Makers
      griffithlab/Immuno_Workflow_Course
      fhdsl/Intro_to_R
      fhdsl/Intro_to_Command_Line
      fhdsl/Intro_to_Git_GitHub
      fhdsl/WDL_Workflows_Guide
      fhdsl/Intermediate-Git-GitHub
      fhdsl/GitHub_Automation_for_Scientists
      williamtmillsiv/introduction_to_bioinformatics
      fhdsl/OTTR_Quarto
      fhdsl/bench_to_bytes
      fhdsl/Intermediate_R
      fhdsl/DataViz_Practice
      fhdsl/DataViz_Considerations
      fhdsl/Intro_to_Python
      fhdsl/Containers_for_Scientists
      acmadeo/GARDE_try2
      fhdsl/Intermediate_Python
###ADD NEW REPO HERE following the format above#
       
### These are custom groups for syncing -- not all files needs to be synced
  - files:
    - source: config_automation.yml
      dest: config_automation.yml
    - source: .github/workflows/pull-request.yml
      dest: .github/workflows/pull-request.yml
    repos: |
      jhudsl/OTTR_Template_Website

  - files:
    - source: config_automation.yml
      dest: config_automation.yml
    - source: .github/workflows/delete-preview.yml
      dest: .github/workflows/delete-preview.yml
    - source: .github/workflows/send-updates.yml
      dest: .github/workflows/send-updates.yml
    - source: .github/workflows/test-send-updates.yml
      dest: .github/workflows/test-send-updates.yml
    - source: scripts/make_screenshots.R
      dest: scripts/make_screenshots.R
    - source: scripts/switch_sync_repo.R
      dest: scripts/switch_sync_repo.R
    - source: config_automation.yml
      dest: config_automation.yml
    repos: |
      jhudsl/OTTR_Quizzes

  - files:
    - source: .github/workflows/
      dest: .github/workflows/
      exclude: |
        starting-course.yml
        release-notes.yml
    - source: .github/switch_sync_repo.R
      dest: .github/switch_sync_repo.R
    - source: .github/ISSUE_TEMPLATE/course-problem-report.md
      dest: .github/ISSUE_TEMPLATE/course-problem-report.md
    - source: .github/ISSUE_TEMPLATE/course-content-add.md
      dest: .github/ISSUE_TEMPLATE/course-content-add.md
    - source: code_of_conduct.md
      dest: code_of_conduct.md
    - source: assets/box_images/
      dest: assets/box_images/
    - source: assets/style.css
      dest: assets/style.css
    - source: assets/toc_close.css
      dest: assets/toc_close.css
    - source: scripts/
      dest: scripts/
      deleteOrphaned: true
    - source: style-sets/fhdasl/
      dest: style-sets/fhdasl/
    - source: config_automation.yml
      dest: config_automation.yml
    repos: |
      jhudsl/AnVIL_Template

  - files:
    - source: config_automation.yml
      dest: config_automation.yml
    - source: .github/workflows/
      dest: .github/workflows/
      deleteOrphaned: true
    - source: .github/switch_sync_repo.R
      dest: .github/switch_sync_repo.R
    - source: .github/automatic-issues/
      dest: .github/automatic-issues/
    - source: assets/box_images/
      dest: assets/box_images/
    - source: assets/style.css
      dest: assets/style.css
    - source: assets/toc_close.css
      dest: assets/toc_close.css
    - source: scripts/
      dest: scripts/
    - source: config_automation.yml
      dest: config_automation.yml
      deleteOrphaned: true
    repos: |
      C-MOOR/C-MOOR_Template

  - files:
    - source: config_automation.yml
      dest: config_automation.yml
    - source: .github/workflows/
      dest: .github/workflows/
      deleteOrphaned: true
    - source: .github/switch_sync_repo.R
      dest: .github/switch_sync_repo.R
    - source: assets/box_images/
      dest: assets/box_images/
    - source: scripts/
      dest: scripts/
      deleteOrphaned: true
    - source: config_automation.yml
      dest: config_automation.yml
    repos: |
      opencasestudies/OCS_Guide