Test PR for nf-core modules lint (#414)

* Update functions.nf for publish_by_id

* Pass a list of publish_by_id instead of a string

* Remove NF version

* Rename code linting file

* Run separate workflow for nf-core modules lint

* Adjust nf-core update comment

* Comment out linting from pytest-workflow.yml

* Remove commented out linting code from pytest-workflow.yml

* Adjust spacing

* Adjust spacing again

* Move NF version to job level for linting

* Add CAPSULE_LOG none env when installing NF

* Remove NXF_ANSI_LOG env for linting

* Revert changes

.github/workflows/nf-core-linting.yml

@@ -0,0 +1,75 @@
+name: nf-core linting
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
+on: [push, pull_request]
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      modules: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: 'tests/config/pytest_software.yml'
+
+  lint:
+    runs-on: ubuntu-20.04
+    env:
+      NXF_VER: 21.03.0-edge
+
+    name: ${{ matrix.tags }}
+    needs: changes
+    if: needs.changes.outputs.modules != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+
+      - name: Install pip
+        run: python -m pip install --upgrade pip
+
+        # FIXME: Remove this when nf-core modules lint stabilizes and install stable release
+      - name: Install nf-core tools development version
+        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Install Nextflow
+        env:
+          CAPSULE_LOG: none
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Lint ${{ matrix.tags }}
+        run: nf-core modules lint . -t ${{ matrix.tags }}
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}

.github/workflows/pytest-workflow.yml

@@ -10,6 +10,7 @@ jobs:
       modules: ${{ steps.filter.outputs.changes }}
     steps:
       - uses: actions/checkout@v2
+
       - uses: dorny/paths-filter@v2
         id: filter
         with:
@@ -17,23 +18,26 @@ jobs:
 
   test:
     runs-on: ubuntu-20.04
+
     name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
     needs: changes
     if: needs.changes.outputs.modules != '[]'
     strategy:
       fail-fast: false
       matrix:
-        nxf_version: ['20.11.0-edge', '21.03.0-edge']
+        nxf_version: ['21.03.0-edge']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
         profile: ['docker', 'singularity', 'conda']
     env:
       NXF_ANSI_LOG: false
     steps:
       - uses: actions/checkout@v2
+
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
           python-version: "3.x"
+
       - uses: actions/cache@v2
         with:
           path: ~/.cache/pip
@@ -45,14 +49,9 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: "3.x"
-      - name: Install dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
-        # FIXME: Remove this when nf-core modules lint stabilizes
-      - name: Install nf-core tools development version
-        run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
 
-      - name: Lint ${{ matrix.tags }}
+      - name: Install Python dependencies
-        run: nf-core modules lint . -t ${{ matrix.tags }}
+        run: python -m pip install --upgrade pip pytest-workflow
 
       - uses: actions/cache@v2
         with:
@@ -64,11 +63,11 @@ jobs:
       - name: Install Nextflow
         env:
           NXF_VER: ${{ matrix.nxf_version }}
+          CAPSULE_LOG: none
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-
       - name: Set up Singularity
         if: matrix.profile == 'singularity'
         uses: eWaterCycle/setup-singularity@v5
@@ -82,6 +81,7 @@ jobs:
           auto-update-conda: true
           channels: conda-forge,bioconda,defaults
           python-version: ${{ matrix.python-version }}
+
       - name: Conda clean
         if: matrix.profile == 'conda'
         run: conda clean -a