JSON schema: Proteinfold

[lee-t]

Update JSON schema to validate inputs:

• [x] Fork the pipeline to your user account, if you have not done so before (Make sure you deselect Copy the master branch only)
• [x] Go to the dev branch and sync the upstream changes (Sync fork -> Update branch)
• [x] Create a branch called json-schema-improvements with the dev branch as base in the fork
• [x] Open the json-schema-improvements branch of the fork either locally (git clone) or online (via Github Codespaces, GitPod...)
• [x] Open the nextflow_schema.json file
• [x] 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
• [x] Check the schema for insufficient validation keywords and error messages. See the guide for more information on this
• [x] Do the same thing for assets/schema_input.json
• [x] Run nextflow run [main.nf](http://main.nf/) -profile test,docker --outdir results -stub to check for any failures in validation with the basic test setup
• [x] Update the changelog of the pipeline <-not doing this because this is a super minor change
• [x] Push all changes to your fork (if you have not done so yet)
• [x] 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: <ADD A LINK TO THE PR HERE>)
• [ ] Wait for approval and merge the pull request once everything works again
• [ ] Set the issue status to Done

[lee-t]

Lots of downstream updates necessary. Need to change input handling for 3 workflows in this pipeline. Might revisit with nf-schema 2.4

[lee-t]

Ignore my earlier comment, i realize some of the dev branches have already migrated to the latest nf-tools version.

[lee-t]

https://github.com/nf-core/proteinfold/pull/269

[keiran-rowell-unsw]

Closed in dev in #269 as stated.