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Zenodo

Submit a pipeline to Zenodo in order to create a DOI for publication.

Use the link for full information, summarized below: https://www.youtube.com/watch?v=A9FGAU9S9Ow

Prepare GitHub Repository

The GitHub repository should include the following:

  1. README page
  2. Documentation page, such as mkdocs, with usage and contact information
  3. A citation CITATION.cff; Example here
  4. Tagged and versioned, stable repository

  1. Go to Zenodo

  2. Select username in the top right >> Profile. Select `GitHub``

  3. Click Sync Now (top right) to update repos. NOTE: You may have to refresh the page

  4. Toggle the On button on the repo you wish to publish. This will move the pipeline to the Enable Repositories list.

Prepare GitHub Repo

  1. Go to GitHub and find the repository page.

  2. Select Releases >> Draft a new release

  3. Create a tag, following naming semantics described here

  4. Describe the tag with the following: "Connecting pipeline to Zenodo"

Update Zenodo Information

  1. Go to Zenodo

  2. Select My dashboard >> Edit

  3. Update the following information:

    • Resource Type: Software
    • Title: Full Pipeline Name (ShorthandName) (IE Mouse nEoanTigen pRedictOr (METRO)
    • Creators: Add creators, including ORCID's whenever possible
    • Description: A short description of the main features of the pipeline
    • Additional Description: If you use this software, please cite it as below.
    • Keywords and subjects: Add several keywords related to the pipeline
    • Version: add the version used in GitHub
    • Publisher: Zenodo
    • Related works: "Is original form of" "github website" URL

Add DOI, citation to GitHub

  1. Go to Zenodo

  2. Select username in the top right >> Profile. Select `GitHub``

  3. Click Sync Now (top right) to update repos. NOTE: You may have to refresh the page

  4. Copy the DOI for the repository

  5. Return to the GitHub repository and edit the README of the GitHub repo, adding the DOI link.

  6. Update the CITATION.cff as needed.

  7. Create a new tagged version.