nf-core / nf-core/pixelator

JSON schema: Pixelator

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#130 0 comments 0 reactions 1 assignee View on GitHub

@milenaabernardi is already working on this.

Since Mar 26, 2025.

  • #129 by @milenaabernardi — closed without merging
Dominant language
Nextflow
Stars
15
Forks
11
Avg merge
1d 17h
Merged PRs (30d)
11

Description

  • Fork the pipeline to your user account, if you have not done so before (Make sure you deselect Copy the master branch only)
  • Go to the dev branch and sync the upstream changes (Sync fork -> Update branch)
  • Create a branch called json-schema-improvements with the dev branch as base in the fork
  • Open the json-schema-improvements branch of the fork either locally (git clone) or online (via Github Codespaces, GitPod...)
  • Open the nextflow_schema.json file
  • Check that the value in "$schema" is "https://json-schema.org/draft/2020-12/schema". The pipeline should be updated to nf-schema if this is not the case. See the migration guide on how to do this
  • Check the schema for insufficient validation keywords and error messages. See the guide for more information on this
  • Do the same thing for assets/schema_input.json
  • Run nextflow run main.nf -profile test,singularity --outdir results -stub to check for any failures in validation with the basic test setup
  • Update the changelog of the pipeline
  • Push all changes to your fork (if you have not done so yet)
  • Open a pull request to the dev branch of the nf-core repository
  • Request a review in #hackathon-mar-2025-json-schema-improvements or in the pipeline channel (e.g. #sarek for nf-core/sarek) and set the issue status to Ready to review (PR: https://github.com/nf-core/pixelator/pull/129)
  • Wait for approval and merge the pull request once everything works again
  • Set the issue status to Done

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

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