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chore(deps): bump snakemake/snakemake-github-action from 1.25.1 to 2.0.1 #690

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chore(deps): bump snakemake/snakemake-github-action from 1.25.1 to 2.0.1 #690

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10 changes: 5 additions & 5 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ jobs:
steps:
- uses: actions/checkout@v4
- name: Lint workflow
uses: snakemake/snakemake-github-action@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
with:
directory: .
snakefile: workflow/Snakefile
Expand Down Expand Up @@ -155,14 +155,14 @@ 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@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
with:
directory: .tests
snakefile: workflow/Snakefile
args: "-p --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@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
if: startsWith(matrix.rule, 'all -np') != true
with:
directory: .tests
Expand Down Expand Up @@ -347,14 +347,14 @@ 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@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
with:
directory: .tests
snakefile: workflow/Snakefile
args: "-p --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@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
if: startsWith(matrix.rule, 'all -np') != true
with:
directory: .tests
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/release-please.yml
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Expand Up @@ -111,7 +111,7 @@ jobs:

- name: Create Dockerfile
if: ${{ steps.release.outputs.release_created == 'true' }}
uses: snakemake/snakemake-github-action@v1.25.1
uses: snakemake/snakemake-github-action@v2.0.1
with:
directory: .
snakefile: workflow/Snakefile
Expand Down
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