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improve CI #584

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Jun 9, 2022
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improve CI #584

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9144818
improve CI
maxulysse Jun 9, 2022
91516b5
update CHANGELOG [skip ci]
maxulysse Jun 9, 2022
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9 changes: 8 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -54,6 +54,7 @@ jobs:
- "split_fastq"
- "targeted"
- "tumor_normal_pair"

steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -68,15 +69,21 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
nextflow self-update

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"

- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with tests settings
run: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
uses: Wandalen/wretry.action@v1.0.11
with:
command: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3

- name: Output log on failure
if: failure()
run: |
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -72,7 +72,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#334](https://github.com/nf-core/sarek/pull/334) - Sync `dsl2` and `dev` branches
- [#342](https://github.com/nf-core/sarek/pull/342) - Update `README.md`
- [#386](https://github.com/nf-core/sarek/pull/386) - Annotation is back
- [#410](https://github.com/nf-core/sarek/pull/410), [#412](https://github.com/nf-core/sarek/pull/412) - Update `CI` tests
- [#410](https://github.com/nf-core/sarek/pull/410), [#412](https://github.com/nf-core/sarek/pull/412), [#584](https://github.com/nf-core/sarek/pull/584) - Update `CI` tests
- [#418](https://github.com/nf-core/sarek/pull/418) - Fix `known_sites` channels
- [#432](https://github.com/nf-core/sarek/pull/432), [#457](https://github.com/nf-core/sarek/pull/457) - Sort before `tabix index`
- [#454](https://github.com/nf-core/sarek/pull/454) - Input is optional (can actually be found automatically by `Sarek` if previously run)
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