Add testing workflow

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+name: Tests
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        nextflow_version: ["21.04.3", "23.10.1"]
+    name: Run tests
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - name: Create Artifacts Directory
+      run: mkdir artifacts
+    - name: Install Miniconda
+      run: bash .github/scripts/install_conda.sh
+    - name: Install Nextflow
+      env:
+        NXF_VER: ${{ matrix.nextflow_version }}
+      run: bash .github/scripts/install_nextflow.sh
+    - name: Create ART Read-Simulation Environment
+      run: bash .github/scripts/create_art_environment.sh
+    - name: Download Assemblies
+      run: bash .github/scripts/download_assemblies.sh
+    - name: Simulate Reads
+      run: bash .github/scripts/simulate_reads.sh
+    - name: Run Pipeline
+      run: bash .github/scripts/run_pipeline.sh
+    - name: Create Output Checking Environment
+      run: bash .github/scripts/create_output_checking_environment.sh
+    - name: Check Outputs
+      run: bash .github/scripts/check_outputs.sh
+    - name: Prepare Artifacts
+      if: always()
+      run: bash .github/scripts/prepare_artifacts.sh
+    - name: Upload Artifacts
+      uses: actions/upload-artifact@v4
+      if: always()
+      with:
+        name: artifacts-BCCDC-PHL-fluviewer-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }}
+        path: artifacts

.gitignore

@@ -3,8 +3,10 @@
 .github/data/fluviewer_db
 .nextflow*
 work
-test*
+test_input
+test_output
 test_data/
+./test*
 ref/
 input_test/
 output_test/