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Update changelog with JSON schema improvements #459

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Update changelog with JSON schema improvements #459

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f8a9078
Update changelog with JSON schema improvements
ftamiro Mar 26, 2025
2362491
Remove default values for macs_fdr and macs_pvalue to match nextflow.…
ftamiro Mar 26, 2025
8613152
Apply Prettier formatting to pass pre-commit hook
ftamiro Mar 27, 2025
d7db1c2
Implementing suggestions to nextflow_schema.json
ftamiro Apr 14, 2025
6151424
Refine JSON schema for FastQ file validation and update email pattern
ftamiro Apr 14, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
- Updated pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0).
- [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.
- [PR #459](https://github.com/nf-core/chipseq/pull/459) - Improve JSON schema validation for nextflow_schema.json and schema_input.json

### Parameters

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5 changes: 3 additions & 2 deletions assets/schema_input.json
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Expand Up @@ -18,13 +18,14 @@
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"errorMessage": "GZIP-compressed FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"errorMessage": "GZIP-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{
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@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

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