Core Checklists

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New pipeline proposals and onboarding

Instructions for nf-core pipeline approval:

1. Core: Before leaving your feedback(!), update the project status on the issue to ‘Proposed’.
2. 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
3. Core: Make final decision
   • If accepted: update the Project status on the issue ‘Accepted’ section
   • If not accepted: update the project status to ‘turned down’
4. Core: Check proposal has received approval in nf-core/proposals from either:
   • Two members of the core team.
   • One member of the core team and one member of the maintainers team.
5. Core: Verify that the pipeline name follows the pipeline naming guidelines.
6. Core: Create a slack channel with approved pipeline name.
   • Inform the new developer of the next steps
7. Core: Add the main developers to
   • #pipeline-maintainers
   • #release-review-trading channel.
8. Core: Create a branch with the pipeline name in the nf-core/test-datasets repository.
9. Core/Dev: Create the git repository using nf-core pipelines create and push it to GitHub.
10. Core/Dev: Once first release (mostly) ready: 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.

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.

Repository transfer to nf-core organisation

1. Request repository ownership transfer from the developer.

   1. If the repository is under an organisation account, ask the developer to add a core team member as a co-owner.
   2. If the repository is under a personal user account, ask the developer to transfer ownership directly to a core team member’s personal account.
2. Transfer the repository to the nf-core organisation.

   1. In the repository, go to Settings.
   2. Scroll to the bottom of the General page.
   3. Select Transfer, next to Transfer ownership.
   4. Confirm or update the repository name if needed.
3. Configure repository settings in the nf-core organisation.

   1. Ask Matthias for the repository ruleset JSON files (these are still under development, but pinned in the core channel).
   2. In the repository, go to Settings.
   3. In the left sidebar, select Rules (under Code and automation).
   4. Select New ruleset.
   5. Select Import a ruleset, then select one of the JSON files.
   6. Select Create at the bottom of the page. Do not modify any fields.
   7. Repeat the import (step 5) and create (step 6) steps for each JSON file provided.

Making custom docker containers for modules

Instructions for adding custom docker containers to the nf-core https://quay.io organisation.

1. Check with the module author to ensure there is no available solution via Conda, Bioconda, or BioContainers.

2. Ask the module author to:

   • Place a Dockerfile alongside the module (sub)directories
   • Add a README.md describing why the container is needed, and provide instructions for building the container
   • (Optional) add a .gitgnore file to ensure build artefacts are not pushed with the Dockerfile and README.md

3. Ensure Docker is correctly authenticated for pushing to quay.io.

   docker login --username <QUAY_USER_NAME> quay.io

4. Build the Docker image locally and tag it appropriately:

   docker build . -t quay.io/nf-core/<TOOL>:<VERSION>

5. Push the built container image:

   docker push quay.io/nf-core/<TOOL>:<VERSION>

6. Share the container reference with the module author so they can update the module:

   container "nf-core/<TOOL>:<VERSION>"

   Note

   This replaces the entire Docker/Singularity condition in the module.

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