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 6397d07..05912d8 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 }} @@ -28,7 +29,7 @@ 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 +56,7 @@ 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 @@ -82,7 +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@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile" @@ -92,7 +93,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Run analysis - uses: snakemake/snakemake-github-action@v2 + uses: snakemake/snakemake-github-action@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile" @@ -103,7 +104,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Create report - uses: snakemake/snakemake-github-action@v2 + uses: snakemake/snakemake-github-action@v2.0.3 with: directory: "." snakefile: "workflow/Snakefile" @@ -113,8 +114,7 @@ jobs: pip install snakemake-storage-plugin-http - name: Upload report as artifact - - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v5 with: name: report path: report.zip 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 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