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Re-enable schema linting #354

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merged 2 commits into from
Aug 12, 2024
Merged

Re-enable schema linting #354

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6da0787
Re-enable schema linting
grst Aug 12, 2024
c918195
Add missing options to nextflow.config
grst Aug 12, 2024
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3 changes: 0 additions & 3 deletions .nf-core.yml
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Expand Up @@ -6,6 +6,3 @@ lint:
- .github/ISSUE_TEMPLATE/bug_report.yml
files_exist:
- lib/Utils.groovy
# TODO This is because of an issue with the monochromeLogs parameter
# See nextflow.config for details
schema_params: False
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

- Re-enable linting check for nextflow schema ([#354](https://github.com/nf-core/scrnaseq/pull/354))
- Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
- Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
- Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
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7 changes: 2 additions & 5 deletions nextflow.config
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Expand Up @@ -19,6 +19,8 @@ params {
genome = null
transcript_fasta = null
txp2gene = null
fasta = null
gtf = null

// salmon alevin parameters (simpleaf)
simpleaf_rlen = 91
Expand Down Expand Up @@ -114,11 +116,6 @@ params {
validationShowHiddenParams = false
validate_params = true

// TODO temporary workaround a warning
// not used anywhere and should not be necessary anymore after a nf-validation plugin update
// TODO when removing this, also remove the ignored lint check from .nf-core.yml
monochromeLogs = null

}

// Load base.config by default for all pipelines
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