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Work on testing pipeline #14

Work on testing pipeline

Work on testing pipeline #14

Workflow file for this run

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" <- Failing due to 'conda.useMamba = true'. Issue is in test environment. Revisit
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