Add testing workflow (#8) #9
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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: ${{ matrix.nextflow_version }} | |
run: bash .github/scripts/install_nextflow.sh | |
- name: Create ART Short Read Simulation Environment | |
run: bash .github/scripts/create_art_environment.sh | |
- name: Create Badread Long Read Simulation Environment | |
run: bash .github/scripts/create_badread_environment.sh | |
- name: Download Assemblies | |
run: bash .github/scripts/download_assemblies.sh | |
- name: Simulate Short Reads | |
run: bash .github/scripts/simulate_short_reads.sh | |
- name: Simulate Long Reads | |
run: bash .github/scripts/simulate_long_reads.sh | |
- name: Create plassembler environment | |
run: bash .github/scripts/create_plassembler_environment.sh | |
- name: Create plassembler db | |
run: bash .github/scripts/create_plassembler_db.sh | |
- name: Run Pipeline | |
run: bash .github/scripts/run_pipeline.sh | |
- name: Create Output Checking Environment | |
run: bash .github/scripts/create_output_checking_environment.sh | |
- name: Check Outputs | |
run: bash .github/scripts/check_outputs.sh | |
- name: Prepare Artifacts | |
if: always() | |
run: bash .github/scripts/prepare_artifacts.sh | |
- name: Upload Artifacts | |
uses: actions/upload-artifact@v4 | |
if: always() | |
with: | |
name: artifacts-BCCDC-PHL-tbprofiler-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }} | |
path: artifacts |