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add spell checker workflow
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nleroy917 committed Mar 29, 2024
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15 changes: 15 additions & 0 deletions .github/workflows/spellcheck.yaml
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name: Run spell checker
on:
push:
branches:
- master
pull_request:
branches:
- master

jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: crate-ci/typos@v1.19.0
3 changes: 2 additions & 1 deletion docs/pephub/user/pipelines.md
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Expand Up @@ -29,4 +29,5 @@ for sample in pep['items']:
subprocess.run(f"gatk BaseRecalibrator -I {file_path} -R /path/to/{genome}.fa")
```

This is a simple example, but you can see how you can use the PEP to manage your samples and easily integrate them into your workflows. You can use the PEPhub API to get the PEP and then iterate over the samples to run your commands.
This is a simple example, but you can see how you can use the PEP to manage your samples and easily integrate them into your workflows. You can use the PEPhub API to get the PEP and then iterate over the samples to run your commands.

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