Skip to content

Merge branch 'main' of https://github.com/ViralVerity/DENV_pipeline #110

Merge branch 'main' of https://github.com/ViralVerity/DENV_pipeline

Merge branch 'main' of https://github.com/ViralVerity/DENV_pipeline #110

name: denv_pipeline
on: [push, pull_request]
defaults:
run:
shell: bash -el {0}
jobs:
run_pipeline_tests:
name: analysis_pipeline test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest"]
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v2
with:
environment-file: environment.yml
activate-environment: analysis_env
channels: conda-forge,bioconda,defaults
miniconda-version: "latest"
- name: install pipeline
run: pip install -e .
- name: run_dry_run
working-directory: tests
run: denv_pipeline --config dry_run_config.yml --dry-run
- name: test_setup
working-directory: tests
run: python scripts/unit_tests_dry_run.py
\--in-config dry_run_config.yml
\--out-config test_output_dry_run/output_config.yml
\--outdir test_output_dry_run
- name: install snakemake dependencies
run: python -m pip install --upgrade pip pandas
- name: run_full
working-directory: tests
run: denv_pipeline --config base_run_config.yml
- name: test_results
working-directory: tests
run: python scripts/unit_tests_results.py
\--outdir test_output_full_run/results
\--depth 10