Migrate CI tests to nf-test

.github/workflows/ci.yml

@@ -1,10 +1,9 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
+  pull_request:
     branches:
       - dev
-  pull_request:
   release:
     types: [published]
 
@@ -13,7 +12,7 @@ env:
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: Run default pipeline test
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
     runs-on: ubuntu-latest
@@ -22,113 +21,79 @@ jobs:
         NXF_VER:
           - "21.10.3"
           - "latest-everything"
+        test:
+          - "default"
+        profile: ["docker"]
+        exclude:
+          - NXF_VER: "latest-everything"
+            profile: "conda"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: Set up Python
+        uses: actions/setup-python@v2
         with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-  star_salmon:
-    name: Test STAR Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--skip_trimming"
-          - "--gtf false"
-          - "--star_index false"
-          - "--transcript_fasta false"
-          - "--min_mapped_reads 90"
-          - "--with_umi"
-          - "--with_umi --skip_trimming"
-          - "--remove_ribo_rna --skip_qualimap"
-          - "--bam_csi_index"
-          - "--save_align_intermeds --save_reference"
-          - "--featurecounts_group_type false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+          python-version: "3.x"
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
 
-      - name: Run pipeline with STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
 
-  star_rsem:
-    name: Test STAR RSEM with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--rsem_index false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
 
       - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Run pipeline with RSEM STAR and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
-  hisat2:
-    name: Test HISAT2 with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc"
-          - "--hisat2_index false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
 
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
 
-      - name: Run pipeline with HISAT2 and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
 
-  salmon:
-    name: Test Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--skip_qc --skip_alignment"
-          - "--salmon_index false --transcript_fasta false"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+      - name: Run pipeline with tests settings
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag default --symlink --kwdof --git-aware --color=yes
 
-      - name: Install Nextflow
+      - name: Output log on failure
+        if: failure()
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
 
-      - name: Run pipeline with Salmon and various parameters
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity

.github/workflows/pytest-workflow.yml

@@ -0,0 +1,109 @@
+name: pytest-workflow
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  pull_request:
+    branches:
+      - dev
+
+env:
+  NXF_ANSI_LOG: false
+
+jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/pytest_tags.yml"
+
+  test_changes:
+    name: ${{ matrix.tags }} ${{ matrix.profile }}
+    runs-on: ubuntu-20.04
+    needs: changes
+    if: needs.changes.outputs.tags != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile: ["docker"] # TODO Add singularity/conda
+    steps:
+      - name: Check out pipeline code
+        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: Install Python dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      - uses: actions/cache@v2
+        with:
+          path: /usr/local/bin/nextflow
+          key: ${{ runner.os }}
+          restore-keys: |
+            ${{ runner.os }}-nextflow-
+
+      - name: Install Nextflow
+        env:
+          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
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      # Test the module
+      - name: Run pytest-workflow
+        # only use one thread for pytest-workflow to avoid race condition on conda cache.
+        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt-get install bat > /dev/null
+          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-${{ matrix.profile }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity