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snpeff_db a string not a number #1143

Merged
merged 8 commits into from
Jul 6, 2023
Merged

snpeff_db a string not a number #1143

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63d30f7
it's a string
maxulysse Jul 5, 2023
bbe9c3f
update CHANGELOG
maxulysse Jul 5, 2023
6c03e96
add snpeff_db to schema ignore list
maxulysse Jul 5, 2023
824b6c5
Merge branch 'dev' of github.com:nf-core/sarek into snpeff
maxulysse Jul 6, 2023
a0d4081
mode lenient for schema validation
maxulysse Jul 6, 2023
ba95065
fix lint
maxulysse Jul 6, 2023
4f7490a
sort
maxulysse Jul 6, 2023
851e11e
[automated] Fix linting with Prettier
nf-core-bot Jul 6, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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.
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3 changes: 1 addition & 2 deletions nextflow.config
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -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`.",
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