Work on testing pipeline #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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 |