diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cdc6de93..bc7fa4c7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -83,7 +83,7 @@ jobs: - name: Upload log file artifact if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: nf-test-workdir path: .nf-test/ diff --git a/.nf-core.yml b/.nf-core.yml index 42ea59f0..b6ad47c7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -43,4 +43,4 @@ template: skip_features: - fastqc - is_nfcore - version: 1.9.2 + version: 1.9.3 diff --git a/CHANGELOG.md b/CHANGELOG.md index 598faa39..7a96d2ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.10.0dev + +## v1.9.3 Nifty Nieuwkerke - [January 23 2025] + +1. Fix db postprocess in vcf2db module + ## v1.9.2 - New Nieuwkerke - [January 22 2025] ## Changes diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index a23204b2..fdc641ad 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -29,6 +29,12 @@ process VCF2DB { ${prefix}.db \\ $args + sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' + sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' + sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' + sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' + sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' + cat <<-END_VERSIONS > versions.yml "${task.process}": vcf2db: $VERSION diff --git a/modules/nf-core/vcf2db/vcf2db.diff b/modules/nf-core/vcf2db/vcf2db.diff index 45757135..524bb0db 100644 --- a/modules/nf-core/vcf2db/vcf2db.diff +++ b/modules/nf-core/vcf2db/vcf2db.diff @@ -12,6 +12,19 @@ Changes in 'vcf2db/main.nf': // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" +@@ -29,6 +29,12 @@ + ${prefix}.db \\ + $args + ++ sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' ++ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' ++ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' ++ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' ++ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' ++ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vcf2db: $VERSION 'modules/nf-core/vcf2db/tests/main.nf.test.snap' is unchanged 'modules/nf-core/vcf2db/tests/tags.yml' is unchanged diff --git a/nextflow.config b/nextflow.config index 36bd916e..46ab76ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data""" mainScript = 'main.nf' nextflowVersion = '!>=24.10.0' - version = '1.9.2' + version = '1.9.3' doi = '' }