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fix: update samtools.yaml to latest 1.17 and update github actions #75

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Aug 16, 2023
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18 changes: 9 additions & 9 deletions .github/workflows/main.yml
Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,9 @@ jobs:
formatting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v3
- name: Formatting
uses: github/super-linter@v4
uses: github/super-linter@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: main
Expand All @@ -52,9 +52,9 @@ jobs:
linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v3
- name: Linting
uses: snakemake/snakemake-github-action@v1.22.0
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
Expand All @@ -68,12 +68,12 @@ jobs:
steps:

- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive

- name: Test workflow
uses: snakemake/snakemake-github-action@v1.23.0
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
Expand All @@ -87,12 +87,12 @@ jobs:
steps:

- name: Checkout repository
uses: actions/checkout@v2
uses: actions/checkout@v3
with:
submodules: recursive

- name: Test 3-prime-workflow
uses: snakemake/snakemake-github-action@v1.23.0
uses: snakemake/snakemake-github-action@v1
with:
directory: .test/3-prime-config
snakefile: workflow/Snakefile
Expand All @@ -101,7 +101,7 @@ jobs:
# TODO: add some kind of test mode to report generation which does not really try to include
# results.
# - name: Test report
# uses: snakemake/snakemake-github-action@v1.22.0
# uses: snakemake/snakemake-github-action@v1
# with:
# directory: .test
# snakefile: workflow/Snakefile
Expand Down
2 changes: 1 addition & 1 deletion workflow/envs/samtools.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- nodefaults

dependencies:
- samtools =1.9
- samtools =1.17
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