From 58811a59bf371c582b4019a9ce491d663a2f064b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 1 Nov 2025 11:19:02 +0000 Subject: [PATCH 1/7] chore(deps): bump the github-actions group across 1 directory with 4 updates Bumps the github-actions group with 4 updates in the / directory: [amannn/action-semantic-pull-request](https://github.com/amannn/action-semantic-pull-request), [8BitJonny/gh-get-current-pr](https://github.com/8bitjonny/gh-get-current-pr), [actions/checkout](https://github.com/actions/checkout) and [actions/upload-artifact](https://github.com/actions/upload-artifact). Updates `amannn/action-semantic-pull-request` from 5.5.3 to 6.1.1 - [Release notes](https://github.com/amannn/action-semantic-pull-request/releases) - [Changelog](https://github.com/amannn/action-semantic-pull-request/blob/main/CHANGELOG.md) - [Commits](https://github.com/amannn/action-semantic-pull-request/compare/v5.5.3...v6.1.1) Updates `8BitJonny/gh-get-current-pr` from 3.0.0 to 4.0.0 - [Release notes](https://github.com/8bitjonny/gh-get-current-pr/releases) - [Commits](https://github.com/8bitjonny/gh-get-current-pr/compare/3.0.0...4.0.0) Updates `actions/checkout` from 4 to 5 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v4...v5) Updates `actions/upload-artifact` from 4 to 5 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v4...v5) --- updated-dependencies: - dependency-name: amannn/action-semantic-pull-request dependency-version: 6.1.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: 8BitJonny/gh-get-current-pr dependency-version: 4.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions - dependency-name: actions/upload-artifact dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major dependency-group: github-actions ... Signed-off-by: dependabot[bot] --- .github/workflows/conventional-prs.yml | 2 +- .github/workflows/main.yml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/conventional-prs.yml b/.github/workflows/conventional-prs.yml index 0dc3b11..0bbe1ba 100644 --- a/.github/workflows/conventional-prs.yml +++ b/.github/workflows/conventional-prs.yml @@ -12,6 +12,6 @@ jobs: title-format: runs-on: ubuntu-latest steps: - - uses: amannn/action-semantic-pull-request@v5.5.3 + - uses: amannn/action-semantic-pull-request@v6.1.1 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 01be770..16ee76c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -28,7 +28,7 @@ jobs: BENCHMARK_GIAB_NA12878_TWIST_TOKEN: ${{ secrets.BENCHMARK_GIAB_NA12878_TWIST_TOKEN }} SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN: ${{ secrets.SNAKEMAKE_STORAGE_ZENODO_ACCESS_TOKEN }} steps: - - uses: 8BitJonny/gh-get-current-pr@3.0.0 + - uses: 8BitJonny/gh-get-current-pr@4.0.0 id: pr with: sha: ${{ github.event.pull_request.head.sha }} @@ -55,7 +55,7 @@ jobs: docker-images: false - name: Check out repository code - uses: actions/checkout@v4 + uses: actions/checkout@v5 - name: Download reference genome uses: snakemake/snakemake-github-action@v2 @@ -114,7 +114,7 @@ jobs: - name: Upload report as artifact - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v5 with: name: report path: report.zip From 028735ca8ed1c08eeebf70162c743e2537523d74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Thu, 6 Nov 2025 11:33:16 +0100 Subject: [PATCH 2/7] try increasing timout --- .github/workflows/main.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 16ee76c..6f7bc14 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -18,6 +18,7 @@ jobs: runs-on: ubuntu-latest permissions: actions: write + env: FTP_PASSWORD: ${{ secrets.FTP_PASSWORD }} ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }} @@ -93,6 +94,7 @@ jobs: - name: Run analysis uses: snakemake/snakemake-github-action@v2 + timeout-minutes: 360 with: directory: "." snakefile: "workflow/Snakefile" @@ -113,7 +115,6 @@ jobs: pip install snakemake-storage-plugin-http - name: Upload report as artifact - uses: actions/upload-artifact@v5 with: name: report From 5ec2407f8771894ae38881f5a878c08f94b821c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 14 Nov 2025 15:41:45 +0100 Subject: [PATCH 3/7] update snakemake to v2.0.1 --- .github/workflows/main.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6f7bc14..de86c95 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -83,7 +83,7 @@ jobs: # because their modification dates are too new or too old. # (as git does not preserve modification dates) - name: Fix modification dates - uses: snakemake/snakemake-github-action@v2 + uses: snakemake/snakemake-github-action@v2.0.1 with: directory: "." snakefile: "workflow/Snakefile" @@ -93,7 +93,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Run analysis - uses: snakemake/snakemake-github-action@v2 + uses: snakemake/snakemake-github-action@v2.0.1 timeout-minutes: 360 with: directory: "." @@ -105,7 +105,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Create report - uses: snakemake/snakemake-github-action@v2 + uses: snakemake/snakemake-github-action@v2.0.1 with: directory: "." snakefile: "workflow/Snakefile" From e9b9a0856654037a56265cb59e71891dfbaa4168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 14 Nov 2025 17:04:15 +0100 Subject: [PATCH 4/7] try setting memory limit --- config/config.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/config/config.yaml b/config/config.yaml index 20f40ce..b5ca5e7 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -779,3 +779,6 @@ custom-benchmarks: limit-regions: activate: false reference-genome: grch38 + +default-resources: + - mem_mb=14336 From a404cad9d2397eddcc2ca4c6a1401017d24816e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Fri, 14 Nov 2025 22:04:19 +0100 Subject: [PATCH 5/7] test: bump to 1.14.0 --- workflow/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 7c07716..90c4c2a 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -18,7 +18,7 @@ module benchmark: github( "snakemake-workflows/dna-seq-benchmark", path="workflow/Snakefile", - tag="v1.13.0", + tag="v1.14.0", ) config: config From efbfc330d5fec38f9e679915da0d8cc3b83812a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= Date: Sun, 16 Nov 2025 13:29:57 +0100 Subject: [PATCH 6/7] remove timeout --- .github/workflows/main.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index de86c95..8a1c883 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -94,7 +94,6 @@ jobs: - name: Run analysis uses: snakemake/snakemake-github-action@v2.0.1 - timeout-minutes: 360 with: directory: "." snakefile: "workflow/Snakefile" From 87ef5dc17c8d7e172e9e5c337d0656111e10344b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bianca=20St=C3=B6cker?= Date: Tue, 16 Dec 2025 14:18:40 +0100 Subject: [PATCH 7/7] chore: Upgrade Snakemake GitHub Action to v2.0.3 --- .github/workflows/main.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 1d319fb..05912d8 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -83,7 +83,7 @@ jobs: # because their modification dates are too new or too old. # (as git does not preserve modification dates) - name: Fix modification dates - uses: snakemake/snakemake-github-action@v2.0.1 + uses: snakemake/snakemake-github-action@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile" @@ -93,7 +93,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Run analysis - uses: snakemake/snakemake-github-action@v2.0.1 + uses: snakemake/snakemake-github-action@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile" @@ -104,7 +104,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Create report - uses: snakemake/snakemake-github-action@v2.0.1 + uses: snakemake/snakemake-github-action@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile"