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chore(deps): bump snakemake/snakemake-github-action from 1.24.0 to 1.25.1 #600

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merged 2 commits into from
Nov 18, 2023
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chore(deps): bump snakemake/snakemake-github-action from 1.24.0 to 1.25.1 #600

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7aff5c4
chore(deps): bump snakemake/snakemake-github-action
dependabot[bot] Oct 31, 2023
8fd5b99
Merge branch 'master' into dependabot/github_actions/snakemake/snakem…
vBassewitz Nov 17, 2023
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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 @@ -41,7 +41,7 @@ jobs:
steps:
- uses: actions/checkout@v4
- name: Lint workflow
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .
snakefile: workflow/Snakefile
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .
snakefile: workflow/Snakefile
Expand Down
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