Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .nf-core.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 3 additions & 1 deletion CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down Expand Up @@ -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

Expand Down
3 changes: 1 addition & 2 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Expand Down
2 changes: 1 addition & 1 deletion nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
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`.",
Expand Down