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ci: Remove Nextflow caching #1202

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merged 4 commits into from
Aug 31, 2023
Merged

ci: Remove Nextflow caching #1202

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f82478d
ci: Remove Nextflow caching
edmundmiller Aug 31, 2023
74a1fb7
ci: Use latest wretry action
edmundmiller Aug 31, 2023
43cefc6
ci: Update setup-python to v4
edmundmiller Aug 31, 2023
83b2647
chore: Update CHANGELOG
edmundmiller Aug 31, 2023
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13 changes: 3 additions & 10 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ jobs:
done;
- name: Set up Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: "3.x"

Expand All @@ -80,15 +80,8 @@ jobs:
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow

- uses: actions/cache@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow ${{ matrix.NXF_VER }}
uses: nf-core/setup-nextflow@v1.2.0
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

Expand All @@ -111,7 +104,7 @@ jobs:
run: conda clean -a

- name: Run pipeline with tests settings
uses: Wandalen/wretry.action@v1.0.11
uses: Wandalen/wretry.action@v1
with:
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3
Expand Down
13 changes: 3 additions & 10 deletions .github/workflows/pytest-workflow.yml
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Expand Up @@ -102,7 +102,7 @@ jobs:
done;
- name: Set up Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: "3.x"

Expand All @@ -116,15 +116,8 @@ jobs:
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow cryptography

- uses: actions/cache@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow ${{ matrix.NXF_VER }}
uses: nf-core/setup-nextflow@v1.2.0
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

Expand Down Expand Up @@ -159,7 +152,7 @@ jobs:
run: conda clean -a

- name: Run pytest-workflow
uses: Wandalen/wretry.action@v1.0.11
uses: Wandalen/wretry.action@v1
with:
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3
Expand Down
13 changes: 3 additions & 10 deletions .github/workflows/pytest-workflow_release.yml
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Expand Up @@ -84,7 +84,7 @@ jobs:
done;
- name: Set up Python
uses: actions/setup-python@v2
uses: actions/setup-python@v4
with:
python-version: "3.x"

Expand All @@ -98,15 +98,8 @@ jobs:
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow

- uses: actions/cache@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow ${{ matrix.NXF_VER }}
uses: nf-core/setup-nextflow@v1.2.0
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

Expand All @@ -129,7 +122,7 @@ jobs:
run: conda clean -a

- name: Run pytest-workflow
uses: Wandalen/wretry.action@v1.0.11
uses: Wandalen/wretry.action@v1
with:
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
attempt_limit: 3
Expand Down
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -52,6 +52,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
- [#1184](https://github.com/nf-core/sarek/pull/1184) - Fix issue with duplicated variants in VCF from Sentieon-based joint-germline variant-calling with VQSR. (Corresponding to [#966](https://github.com/nf-core/sarek/issues/966) for GATK.)
- [#1192](https://github.com/nf-core/sarek/pull/1192) - Add `ASCATprofile.png` to ASCAT output docs
- [#1197](https://github.com/nf-core/sarek/pull/1197) - Improve `tower.yml` file to display reports in `Tower` ([#1190](https://github.com/nf-core/sarek/issues/1190))
- [#1202](https://github.com/nf-core/sarek/pull/1202) - Remove GitHub action step that caches Nextflow. Also bump other out of date actions.

### Dependencies

Expand Down