Be consistent in GHA names, only use Setup, remove Set up or Install #6766
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@@ -44,12 +44,12 @@ jobs: | |||||
| - name: Check out repository | ||||||
| uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 | ||||||
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| - name: Set up NodeJS | ||||||
| uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 | ||||||
| with: | ||||||
| node-version: "20" | ||||||
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| - name: Set up Prettier | ||||||
| run: npm install -g [email protected] | ||||||
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| - name: Run Prettier --check | ||||||
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@@ -64,7 +64,7 @@ jobs: | |||||
| with: | ||||||
| node-version: "20" | ||||||
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| - name: Set up editorconfig-checker | ||||||
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| run: npm install -g editorconfig-checker | ||||||
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| - name: Run ECLint check | ||||||
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@@ -163,18 +163,18 @@ jobs: | |||||
| restore-keys: | | ||||||
| ${{ runner.os }}-pip | ||||||
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| - name: Set up pip | ||||||
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There was a problem hiding this comment. not sure if we actually need this step anymore |
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| run: python -m pip install --upgrade pip | ||||||
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| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | ||||||
| with: | ||||||
| distribution: "temurin" | ||||||
| java-version: "17" | ||||||
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| - name: Set up Nextflow | ||||||
| uses: nf-core/setup-nextflow@v2 | ||||||
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| - name: Set up nf-core tools development version | ||||||
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| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | ||||||
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| - name: Lint module ${{ matrix.tags }} | ||||||
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@@ -201,18 +201,18 @@ jobs: | |||||
| with: | ||||||
| python-version: "3.11" | ||||||
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| - name: Set up pip | ||||||
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| run: python -m pip install --upgrade pip | ||||||
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| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | ||||||
| with: | ||||||
| distribution: "temurin" | ||||||
| java-version: "17" | ||||||
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| - name: Set up Nextflow | ||||||
| uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # v2 | ||||||
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| - name: Set up nf-core tools development version | ||||||
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| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | ||||||
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| - name: Lint module ${{ matrix.tags }} | ||||||
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@@ -413,19 +413,19 @@ jobs: | |||||
| restore-keys: | | ||||||
| ${{ runner.os }}-pip-pytest | ||||||
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| - name: Set up Python dependencies | ||||||
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| run: python -m pip install --upgrade pip pytest-workflow cryptography | ||||||
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| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | ||||||
| with: | ||||||
| distribution: "temurin" | ||||||
| java-version: "17" | ||||||
| - name: Set up Nextflow ${{ matrix.NXF_VER }} | ||||||
| uses: nf-core/setup-nextflow@v2 | ||||||
| with: | ||||||
| version: "${{ matrix.NXF_VER }}" | ||||||
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| - name: Set up apptainer | ||||||
| if: matrix.profile == 'singularity' | ||||||
| uses: eWaterCycle/setup-apptainer@main | ||||||
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@@ -442,7 +442,7 @@ jobs: | |||||
| channels: conda-forge,bioconda | ||||||
| python-version: ${{ matrix.python-version }} | ||||||
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| - name: Set up Conda | ||||||
| run: | | ||||||
| conda clean -a | ||||||
| conda install -n base conda-libmamba-solver | ||||||
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There was a problem hiding this comment. this setup step can be removed if we add the |
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@@ -659,15 +659,15 @@ jobs: | |||||
| with: | ||||||
| distribution: "temurin" | ||||||
| java-version: "17" | ||||||
| - name: Set up Nextflow | ||||||
| uses: nf-core/setup-nextflow@v2 | ||||||
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| - name: Set up nf-test | ||||||
| uses: nf-core/setup-nf-test@v1 | ||||||
| with: | ||||||
| version: ${{ env.NFTEST_VER }} | ||||||
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| - name: Set up apptainer | ||||||
| if: matrix.profile == 'singularity' | ||||||
| uses: eWaterCycle/setup-apptainer@main | ||||||
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@@ -690,7 +690,7 @@ jobs: | |||||
| restore-keys: | | ||||||
| ${{ runner.os }}-pip-pdiff | ||||||
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| - name: Set up Python dependencies | ||||||
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| run: python -m pip install --upgrade pip pdiff cryptography | ||||||
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| - name: Set up miniconda | ||||||
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@@ -701,7 +701,7 @@ jobs: | |||||
| auto-update-conda: true | ||||||
| channels: conda-forge,bioconda | ||||||
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| - name: Set up Conda | ||||||
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| if: matrix.profile == 'conda' | ||||||
| run: | | ||||||
| conda clean -a | ||||||
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this is a install step