Json schema improvements #1528
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Json schema improvements #1528
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nvnieuwk
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Mar 26, 2025
assets/schema_input.json
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| "format": "file-path", | ||
| "exists": true, | ||
| "errorMessage": "GZIP-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", | ||
| "anyOf": [ |
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You can remove this anyOf part and only use the "pattern" keyword that's inside of it
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on it, thanks!
…r improved clarity
nvnieuwk
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Mar 26, 2025
nvnieuwk
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Mar 26, 2025
nvnieuwk
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Mar 26, 2025
nextflow_schema.json
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| "pipelines_testdata_base_path": { | ||
| "type": "string", | ||
| "minLength": 1, | ||
| "pattern": "^(https?://\\S+|/[^\\s]+|\\.{0,2}/[^\\s]+)$", |
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Suggested change
| "pattern": "^(https?://\\S+|/[^\\s]+|\\.{0,2}/[^\\s]+)$", |
This does not need to be a HTTPS URL and can also be a local or cloud file-path. Adding this pattern would restrict this
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You are right, I wanted to make a pattern with an optional https, but it may fail and be too restrictive. I will roll it back.
Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
nvnieuwk
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Some comments, but wow this is really impressive! Well done!
…int in nextflow_schema.json
…to use 'yyyy-MM-dd_HH-mm-ss' format
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Could you please add a motivating description to the PR describing what you've done and why? |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.Description
This PR improves the
nextflow_schema.jsonand theschema_input.jsonfiles for the nf-core/rnaseq pipeline as part of the March 2025 JSON Schema Improvements Hackathon.The main goals of these updates are to enhance schema consistency, improve validation error messages, and clarify the help_text and description fields. These changes aim to make the pipeline easier to configure and provide more informative feedback to users.
We followed the hackathon checklist throughout the process.
All changes were tested using:
nextflow run main.nf -profile test,docker --outdir results -stubThe schema remains valid, and no validation issues were observed.