From 9d1d1754b0cbceb6ae34b4427a4a99474254373a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Tue, 14 Apr 2026 13:20:05 +0200 Subject: [PATCH 1/4] ci: remove test with Snakemake v8 --- .github/workflows/test_v8.yml | 39 ----------------------------------- .test/environment_v8.yaml | 8 ------- README.md | 3 +-- 3 files changed, 1 insertion(+), 49 deletions(-) delete mode 100644 .github/workflows/test_v8.yml delete mode 100644 .test/environment_v8.yaml diff --git a/.github/workflows/test_v8.yml b/.github/workflows/test_v8.yml deleted file mode 100644 index 8fd912d..0000000 --- a/.github/workflows/test_v8.yml +++ /dev/null @@ -1,39 +0,0 @@ -name: Test Sm v8 - -on: - workflow_dispatch: - push: - branches: - - main - - dev - pull_request: - branches: - - "**" - -jobs: - run_test_pipeline: - runs-on: ubuntu-latest - steps: - - name: Checkout repository - uses: actions/checkout@v3 - - name: Setup environment - uses: conda-incubator/setup-miniconda@v3 - with: - channel-priority: strict - activate-environment: snakemake - auto-activate-base: false - miniforge-version: latest - environment-file: .test/environment_v8.yaml - - name: Run test pipeline - shell: bash -el {0} - run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml --use-conda -c1 --conda-frontend conda --keep-going --notemp - - name: Pack logs - if: success() || failure() - shell: bash -el {0} - run: tar czf logs.tar.gz .test/output .snakemake/log - - name: Upload output file - if: success() || failure() - uses: actions/upload-artifact@v4 - with: - name: output-logs - path: logs.tar.gz diff --git a/.test/environment_v8.yaml b/.test/environment_v8.yaml deleted file mode 100644 index 8f4b84c..0000000 --- a/.test/environment_v8.yaml +++ /dev/null @@ -1,8 +0,0 @@ -name: snakemake -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - python==3.11.6 - - snakemake==8.30.0 diff --git a/README.md b/README.md index caaa59b..f675880 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,6 @@ ![Install workflow](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/install.yml/badge.svg) ![Test workflow with Snakemake v7](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v7.yml/badge.svg) -![Test workflow with Snakemake v8](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v8.yml/badge.svg) ![Test workflow with Snakemake v9](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_v9.yml/badge.svg) ![Test workflow with Snakemake v9 and Apptainer](https://github.com/PathoGenOmics-Lab/VIPERA/actions/workflows/test_apptainer.yml/badge.svg) @@ -42,7 +41,7 @@ It supports dependency management through either conda or Apptainer/Singularity, We use continuous integration (CI) to automatically verify that all dependencies install correctly with Snakemake v7.32.4 (see GitHub Action `Install`), and to test that VIPERA runs -successfully with Snakemake v7.32.4, v8.30.0, and v9.1.6 using conda (Actions `Test Sm v[7-9]`). +successfully with Snakemake v7.32.4 and v9.1.6 using conda (Actions `Test Sm v(7|9)`). We also test a containerized workflow with Snakemake v9.1.6 and Apptainer using a [remote image](https://hub.docker.com/r/ahmig/vipera) (Action `Test Sm v9 Apptainer`). This image is automatically updated in every version (Action `Deploy`). From a5ba554734357ac3d46b56d7ac049a63a50be9a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Tue, 14 Apr 2026 13:20:36 +0200 Subject: [PATCH 2/4] ci: update Snakemake v9 minor for tests --- .test/environment_v9.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.test/environment_v9.yaml b/.test/environment_v9.yaml index 2ff55fd..26edd4c 100644 --- a/.test/environment_v9.yaml +++ b/.test/environment_v9.yaml @@ -5,4 +5,4 @@ channels: - defaults dependencies: - python==3.11.6 - - snakemake==9.1.6 + - snakemake==9.15.0 From a69e34cc958ec7def0368c18cbb57a3256b5c801 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Tue, 14 Apr 2026 13:22:26 +0200 Subject: [PATCH 3/4] ci: update Snakemake v9 for apptainer test --- .test/environment_apptainer.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.test/environment_apptainer.yaml b/.test/environment_apptainer.yaml index dc20bb7..e17bee1 100644 --- a/.test/environment_apptainer.yaml +++ b/.test/environment_apptainer.yaml @@ -5,5 +5,5 @@ channels: - defaults dependencies: - python==3.11.6 - - snakemake==9.1.6 + - snakemake==9.15.0 - apptainer==1.4.1 From 8112b119a6f51b8d43d823e01c2dbee956866e2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miguel=20=C3=81lvarez=20Herrera?= Date: Tue, 14 Apr 2026 13:22:42 +0200 Subject: [PATCH 4/4] docs: update Snakemake versions on README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f675880..cf44879 100644 --- a/README.md +++ b/README.md @@ -41,8 +41,8 @@ It supports dependency management through either conda or Apptainer/Singularity, We use continuous integration (CI) to automatically verify that all dependencies install correctly with Snakemake v7.32.4 (see GitHub Action `Install`), and to test that VIPERA runs -successfully with Snakemake v7.32.4 and v9.1.6 using conda (Actions `Test Sm v(7|9)`). -We also test a containerized workflow with Snakemake v9.1.6 and Apptainer using a +successfully with Snakemake v7.32.4 and v9.15.0 using conda (Actions `Test Sm v(7|9)`). +We also test a containerized workflow with Snakemake v9.15.0 and Apptainer using a [remote image](https://hub.docker.com/r/ahmig/vipera) (Action `Test Sm v9 Apptainer`). This image is automatically updated in every version (Action `Deploy`).