ci: Try to install current nf-core tools from repo

nf-core · Oct 12, 2022 · 7e8b1b8 · 7e8b1b8
1 parent 6bd773f
commit 7e8b1b8
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Showing 4 changed files with 21 additions and 21 deletions.
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -24,6 +24,12 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
+      # Set up Nextflow
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: ${{ matrix.NXF_VER }}
+
       # Set up nf-core/tools
       - name: Set up Python 3.8
         uses: actions/setup-python@v3
@@ -35,12 +41,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
-      # Set up Nextflow
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: ${{ matrix.NXF_VER }}
-
       # Install the Prettier linting tools
       - uses: actions/setup-node@v2
 

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -23,6 +23,11 @@ jobs:
       - uses: actions/checkout@v3
         name: Check out source-code repository
 
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: ${{ matrix.NXF_VER }}
+
       - name: Set up Python 3.7
         uses: actions/setup-python@v3
         with:
@@ -33,11 +38,6 @@ jobs:
           python -m pip install --upgrade pip
           pip install .
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: ${{ matrix.NXF_VER }}
-
       - name: Run nf-core/tools
         run: |
           nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -26,16 +26,16 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install python dependencies
-        run: |
-          python -m pip install --upgrade pip -r requirements-dev.txt
-          pip install -e .
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "latest-everything"
 
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
       - name: Test with pytest
         run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core
 

diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -53,16 +53,16 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Install python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
-
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "latest-everything"
 
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+
       - name: Run synchronisation
         if: github.repository == 'nf-core/tools'
         env: