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Update changelog with JSON schema improvements#459

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ftamiro wants to merge 6 commits into
nf-core:devfrom
ftamiro:json-schema-improvements
Open

Update changelog with JSON schema improvements#459
ftamiro wants to merge 6 commits into
nf-core:devfrom
ftamiro:json-schema-improvements

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@ftamiro

@ftamiro ftamiro commented Mar 26, 2025 •
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  • 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,docker --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: )
  • Wait for approval and merge the pull request once everything works again
  • Set the issue status to Done

@github-actions

github-actions Bot commented Mar 26, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 83299b0

+| ✅ 270 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config
  • files_unchanged - File ignored due to lint config: assets/nf-core-chipseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-chipseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-06-30 14:22:15

nvnieuwk
nvnieuwk reviewed Mar 27, 2025
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Comment thread assets/schema_input.json Outdated
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{

@nvnieuwk nvnieuwk Mar 27, 2025

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You can remove this anyOf section and add the keywords from the first section to the root of the fastq_2 parameter

nvnieuwk
nvnieuwk reviewed Mar 27, 2025
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Comment thread nextflow_schema.json Outdated
nvnieuwk
nvnieuwk reviewed Mar 27, 2025
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Comment thread nextflow_schema.json Outdated
nvnieuwk
nvnieuwk reviewed Mar 27, 2025
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Wow, well done! Here are some small comments!

@ftamiro

ftamiro commented Apr 3, 2025

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@nvnieuwk

Wow, well done! Here are some small comments!

Thank you for all the comments! I will review everything and address them in the following days (weekend, April 5-6).

ftamiro and others added 2 commits April 14, 2025 17:15
@ftamiro @nvnieuwk
Implementing suggestions to nextflow_schema.json
d7db1c2 
Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
@ftamiro
Refine JSON schema for FastQ file validation and update email pattern
6151424
@nvnieuwk

nvnieuwk commented Oct 16, 2025

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@ftamiro any updates here?

@JoseEspinosa

JoseEspinosa commented Jun 30, 2026

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@ftamiro @nvnieuwk can we merge this PR?

nvnieuwk
nvnieuwk reviewed Jun 30, 2026
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All good to me if all changes make sense for this pipeline

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@ftamiro @nvnieuwk @JoseEspinosa