diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 1dd78e03..6c466565 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -41,7 +41,7 @@ jobs: steps: - uses: actions/checkout@v2 - name: Lint workflow - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 with: directory: . snakefile: workflow/Snakefile @@ -137,14 +137,14 @@ jobs: curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314997.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.1.7.fasta curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314998.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.351.fasta - name: Test rule ${{ matrix.rule }} on ${{ matrix.technology }} ${{ matrix.seq_method }} data - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 with: directory: .tests snakefile: workflow/Snakefile args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}" - name: Test report - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 if: startsWith(matrix.rule, 'all -npr') != true with: directory: .tests @@ -315,14 +315,14 @@ jobs: curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314997.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.1.7.fasta curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314998.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.351.fasta - name: Test rule ${{ matrix.rule }} - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 with: directory: .tests snakefile: workflow/Snakefile args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}" - name: Test report - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 if: startsWith(matrix.rule, 'all -npr') != true with: directory: .tests diff --git a/.github/workflows/release-please.yml b/.github/workflows/release-please.yml index 2c4b823d..4811207a 100644 --- a/.github/workflows/release-please.yml +++ b/.github/workflows/release-please.yml @@ -111,7 +111,7 @@ jobs: - name: Create Dockerfile if: ${{ steps.release.outputs.release_created == 'true' }} - uses: snakemake/snakemake-github-action@v1.24.0 + uses: snakemake/snakemake-github-action@v1.25.1 with: directory: . snakefile: workflow/Snakefile