From 3a7f5392d8fc961145c54098a400c65d4121e955 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 22 Jan 2025 15:30:21 +0100 Subject: [PATCH 01/10] bump back to dev --- .nf-core.yml | 52 ++++++++++++++++++++++++------------------------- CHANGELOG.md | 2 ++ nextflow.config | 2 +- 3 files changed, 29 insertions(+), 27 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 42ea59f0..81a37031 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,32 +2,32 @@ bump_version: lint: actions_ci: false files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/template_version_comment.yml - - docs/README.md + - CODE_OF_CONDUCT.md + - assets/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - .github/workflows/template_version_comment.yml + - docs/README.md files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - CODE_OF_CONDUCT.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - .prettierignore + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - CODE_OF_CONDUCT.md + - .github/ISSUE_TEMPLATE/bug_report.yml + - .prettierignore multiqc_config: - - report_comment + - report_comment nextflow_config: - - custom_config - - manifest.name - - manifest.homePage - - validation.help.afterText - - validation.summary.afterText + - custom_config + - manifest.name + - manifest.homePage + - validation.help.afterText + - validation.summary.afterText subworkflow_changes: false nf_core_version: 3.0.2 repository_type: pipeline @@ -41,6 +41,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore - version: 1.9.2 + - fastqc + - is_nfcore + version: 1.10.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 598faa39..3892fcc2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ 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 + ## v1.9.2 - New Nieuwkerke - [January 22 2025] ## Changes diff --git a/nextflow.config b/nextflow.config index 36bd916e..669bd9f6 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 = '1.10.0dev' doi = '' } From 3d4e693677d2dcf6dc69c704b340441b203806c6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 22 Jan 2025 19:54:54 +0100 Subject: [PATCH 02/10] add db postprocessing to vcf2db --- modules/nf-core/vcf2db/main.nf | 6 ++++++ modules/nf-core/vcf2db/vcf2db.diff | 13 +++++++++++++ 2 files changed, 19 insertions(+) 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 From c997f5dc09493396e2e49b51aa7b6a8162461cc6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 22 Jan 2025 20:03:11 +0100 Subject: [PATCH 03/10] prettier --- .nf-core.yml | 50 +++++++++++++++++++++++++------------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 81a37031..57742128 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,32 +2,32 @@ bump_version: lint: actions_ci: false files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/template_version_comment.yml - - docs/README.md + - CODE_OF_CONDUCT.md + - assets/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - .github/workflows/template_version_comment.yml + - docs/README.md files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - CODE_OF_CONDUCT.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - .prettierignore + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - CODE_OF_CONDUCT.md + - .github/ISSUE_TEMPLATE/bug_report.yml + - .prettierignore multiqc_config: - - report_comment + - report_comment nextflow_config: - - custom_config - - manifest.name - - manifest.homePage - - validation.help.afterText - - validation.summary.afterText + - custom_config + - manifest.name + - manifest.homePage + - validation.help.afterText + - validation.summary.afterText subworkflow_changes: false nf_core_version: 3.0.2 repository_type: pipeline @@ -41,6 +41,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore + - fastqc + - is_nfcore version: 1.10.0dev From 19758440b0c46ad60e5eed4a7d69e37906888131 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 23 Jan 2025 09:25:20 +0100 Subject: [PATCH 04/10] bump pipeline version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 669bd9f6..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 = '1.10.0dev' + version = '1.9.3' doi = '' } From 1714c7f592a498edd6c22fe00a507c64147d1391 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Thu, 23 Jan 2025 09:26:54 +0100 Subject: [PATCH 05/10] update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3892fcc2..7a96d2ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## 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 From 5cdb99705a5d9489db383e5dedcc59ee4dd3e5e3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 23 Jan 2025 13:26:00 +0100 Subject: [PATCH 06/10] Update .nf-core.yml --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 57742128..b6ad47c7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -43,4 +43,4 @@ template: skip_features: - fastqc - is_nfcore - version: 1.10.0dev + version: 1.9.3 From d2b2c6211116df3087989de2367e43a936bbe78a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 23 Jan 2025 15:56:30 +0100 Subject: [PATCH 07/10] bump to dev --- .nf-core.yml | 52 ++++++++++++++++++++++++------------------------- nextflow.config | 2 +- 2 files changed, 27 insertions(+), 27 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index b6ad47c7..81a37031 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,32 +2,32 @@ bump_version: lint: actions_ci: false files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/template_version_comment.yml - - docs/README.md + - CODE_OF_CONDUCT.md + - assets/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - .github/workflows/template_version_comment.yml + - docs/README.md files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - CODE_OF_CONDUCT.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - .prettierignore + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - CODE_OF_CONDUCT.md + - .github/ISSUE_TEMPLATE/bug_report.yml + - .prettierignore multiqc_config: - - report_comment + - report_comment nextflow_config: - - custom_config - - manifest.name - - manifest.homePage - - validation.help.afterText - - validation.summary.afterText + - custom_config + - manifest.name + - manifest.homePage + - validation.help.afterText + - validation.summary.afterText subworkflow_changes: false nf_core_version: 3.0.2 repository_type: pipeline @@ -41,6 +41,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore - version: 1.9.3 + - fastqc + - is_nfcore + version: 1.10.0dev diff --git a/nextflow.config b/nextflow.config index 46ab76ca..669bd9f6 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 = '1.9.3' + version = '1.10.0dev' doi = '' } From 95e6fecbad646c472af9f9c514e7d1cd0eda6737 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 23 Jan 2025 15:57:53 +0100 Subject: [PATCH 08/10] bumped too soon --- .nf-core.yml | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 81a37031..99e7478b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -43,4 +43,4 @@ template: skip_features: - fastqc - is_nfcore - version: 1.10.0dev + version: 1.9.3 diff --git a/nextflow.config b/nextflow.config index 669bd9f6..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 = '1.10.0dev' + version = '1.9.3' doi = '' } From 9fd509379c0392f98bb671539316ba418cef252c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 23 Jan 2025 16:09:54 +0100 Subject: [PATCH 09/10] update upload artifacts in ci --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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/ From 15836dfe9df6914ceb34dccad40a7576ae33854d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 23 Jan 2025 16:10:57 +0100 Subject: [PATCH 10/10] linting --- .nf-core.yml | 50 +++++++++++++++++++++++++------------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 99e7478b..b6ad47c7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,32 +2,32 @@ bump_version: lint: actions_ci: false files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - .github/workflows/template_version_comment.yml - - docs/README.md + - CODE_OF_CONDUCT.md + - assets/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_light.png + - docs/images/nf-core-germline_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - .github/workflows/template_version_comment.yml + - docs/README.md files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - CODE_OF_CONDUCT.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - .prettierignore + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - CODE_OF_CONDUCT.md + - .github/ISSUE_TEMPLATE/bug_report.yml + - .prettierignore multiqc_config: - - report_comment + - report_comment nextflow_config: - - custom_config - - manifest.name - - manifest.homePage - - validation.help.afterText - - validation.summary.afterText + - custom_config + - manifest.name + - manifest.homePage + - validation.help.afterText + - validation.summary.afterText subworkflow_changes: false nf_core_version: 3.0.2 repository_type: pipeline @@ -41,6 +41,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore + - fastqc + - is_nfcore version: 1.9.3