diff --git a/.nf-core.yml b/.nf-core.yml index 93f9c894b2..6ec4fc101f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -11,4 +11,5 @@ lint: - docs/images/nf-core-sarek_logo_light.png - lib/NfcoreTemplate.groovy - lib/NfcoreSchema.groovy + schema_params: False template_strings: False diff --git a/CHANGELOG.md b/CHANGELOG.md index 9c2c8832b4..10670db8dd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- [#1143](https://github.com/nf-core/sarek/pull/1143) - `snpeff_db` is now a string + ## [3.2.3](https://github.com/nf-core/sarek/releases/tag/3.2.3) - Gällivare Gällivare is a small lake next to Pierikjaure. @@ -1214,7 +1216,7 @@ Ruotes is one of the main massif in the Sarek National Park. - [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to `GATK4` - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG` -- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated ` Nextflow ``$name ` syntax with `withName` +- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated `Nextflow ``$name` syntax with `withName` ### Fixed diff --git a/nextflow.config b/nextflow.config index efc0c029e1..f14ca6fa6a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -126,11 +126,10 @@ params { // Schema validation default options validationFailUnrecognisedParams = false - validationLenientMode = false + validationLenientMode = true validationSchemaIgnoreParams = 'genomes,snpeff_version,vep_version,cf_ploidy' validationShowHiddenParams = false validate_params = true - } // Load base.config by default for all pipelines diff --git a/nextflow_schema.json b/nextflow_schema.json index 6a06cee99a..b6b38d59cb 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -692,7 +692,7 @@ "help_text": "If you use AWS iGenomes, this has already been set for you appropriately." }, "snpeff_db": { - "type": "number", + "type": "string", "fa_icon": "fas fa-database", "description": "snpEff DB version.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the database to be use to annotate with.\nAlternatively databases' names can be listed with the `snpEff databases`.",