Core Checklists

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New pipeline proposals and onboarding

Instructions for nf-core pipeline approval:

1. Core: Before leaving your feedback(!), add to the proposal tracking board under ‘Under discussion’.
2. Core: Add :plus: icon on proposal to know it’s on the board.
3. Community: Discuss benefits/drawbacks of the proposal.
   • Emphasise collaboration (prefer to have more developers on one pipeline rather than one developer).
   • Ensure proposal follows nf-core pipeline guidelines.
   • In some cases, promote ‘partial acceptance’, i.e., if upstream steps already covered in another pipeline, propose new pipeline of just non-overlapping steps
4. Core: Make final decision
   • If accepted: update proposal tracking board, moving proposal to ‘Accepted’ section
   • If not accepted: update proposal tracking board, moving proposal to ‘Turned down’
5. Core: Check proposal has received approval in #new-pipelines from either:
   • Two members of the core team.
   • One member of the core team and one member of the maintainers team.
6. Core: Verify that the pipeline name follows the pipeline naming guidelines.
7. Core: Create a slack channel with approved pipeline name.
8. Core: Ask the developers to join #pipeline-maintainers channel.
9. Core/Dev: Create the git repository using nf-core pipelines create and push it to GitHub.
10. Core/Dev: Transfer the repository to nf-core GitHub organisation and delete the repository on local the machine/user account.
11. Core/Dev: Sync the nf-co.re pipelines page by triggering the GitHub action
    • Website repo > Actions > Build json files and md-cache > Run workflow > From main.
12. Core: Create a branch with the pipeline name in the nf-core/test-datasets repository.

Uploading test data to s3 bucket

Instructions for uploading full-test AWS files for a pipeline to a S3 bucket:

1. Check if the test data is valid so that it can be uploaded:

   Note

   Small input data that may be unreliable when downloaded from other repositories (e.g., limit total file size to a maximum of 10 GB across all files).

2. Check that large files cannot be reduced or subsetted.
3. Select Amazon S3-managed keys (SSE-S3) and create the pipeline directory in the S3 bucket.

Activating Zenodo archiving of a new pipeline

Instructions for setting up Zenodo DOIs.

Before release:

1. Sign up and log in to Zenodo.

2. Select GitHub -> Connect Account in the dropdown menu of your account and connect your GitHub account.

3. Select GitHub in the dropdown menu of your account once connected.

4. Toggle the On switch of the pipeline to enable Zenodo archiving.

   Note

   It’s a good idea to enable this for all active pipelines, as DOIs will only be assigned upon release.

   Note

   Some repositories (e.g., nf-core/exoseq) may not be activated as they are archived.

5. Inform the pipeline developers to make a release.

Post release:

1. Select Github in the dropdown menu of your account in Zenodo and find the relevant repository.
2. Click the Zenodo Record page for the release.
3. Find the Communities box on the record page and submit the record to the nf-core community.
4. Copy the DOI for Cite all versions? in the Versions tab.
5. Update files on the pipeline master branch:
   • README.md: Add the Zenodo Badge and update the If you use this pipeline cite section.
   • Nextflow.config: Update the manifest block to include the DOI.
   • Commit these changes with the message “Add Zenodo ID after first release”.

Adding new community member to the GitHub organisation

Anyone can request to join the nf-core GitHub organisation via the #github-invitations channel.

1. Verify the request is reasonable (i.e., clearly not spam).
2. Send an invitation via nf-core github teams
3. Add new member to the nf-core contributors team
4. Respond to the #github-invitations channel request by reacting with the ✅ emoji.

Updating online bingo cards

Before each hackathon, we need to update the bingo cards to ensure they remain current.

To update the bingo cards:

1. Ask for the outreach google account credentials from @core-team
2. Log into the Firebase Dashboard: https://console.firebase.google.com/
3. Select nfcore-bingo.
4. Select Realtime Database.
5. Select games and navigate down the tree until you reach lexicon.
6. Hover over lexicon and select + to add entries:
   • Key: Number
   • Value: New board entry
7. Select the trash bin next to the given entry to remove it.

Backups

The following items should be regularly backed up by a member of core team with admin access to the relevant service:

• HackMD: backup to Google Drive (Outreach)
• Bingo cards rules JSON (realtime database): backup to Google Drive (Outreach)

New core team member onboarding

This documents the steps that need to be performed when adding a new core team member:

1. Add to core team Slack channel
2. Add to GitHub core team
3. Add as owners on the GitHub org
4. Add to @core-team @outreach-team slack teams
5. Add as admin on slack
6. Add to hackMD team as Admin
7. Add to quay.io in team owners
8. Add to Tower organisation as owner
9. Add to nf-core google calendar(s)
10. Add to core@nf-co.re forwarder
11. Add to Zenodo community as admin
12. Update Website / About (get new member to check)
13. Ask new member to add nf-core apple core emoji as Status
14. Make Slack announcement
15. Make Social media announcement