Revert "[fix] config haplotype generation" #914
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
name: Tests | |
on: | |
push: | |
pull_request: | |
jobs: | |
cancel-previous-jobs: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Cancel Previous Runs | |
uses: styfle/cancel-workflow-action@0.9.1 | |
with: | |
access_token: ${{ github.token }} | |
static_tests: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v2 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: "3.10" | |
mamba-version: "*" | |
channels: conda-forge,bioconda,defaults | |
channel-priority: strict | |
activate-environment: V-pipe | |
auto-update-conda: true | |
- name: Install dependencies | |
run: mamba install --yes snakemake-minimal snakefmt | |
- name: Code formatting | |
run: snakefmt --check . | |
- name: Setup project | |
run: | | |
mkdir -p /tmp/project/hiv/ # virus does not matter | |
cd /tmp/project/hiv/ | |
$GITHUB_WORKSPACE/init_project.sh -n | |
- name: Linting | |
env: | |
PYTHONUNBUFFERED: 1 | |
uses: snakemake/snakemake-github-action@v1.19.0 | |
with: | |
directory: /tmp/project/hiv/ | |
snakefile: 'workflow/Snakefile' | |
args: '--lint' | |
continue-on-error: true # TODO: fix missing cohort consensus | |
runtime_tests: | |
needs: static_tests | |
strategy: | |
max-parallel: 5 | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-latest] | |
python-version: ["3.9", "3.10"] | |
virus: ["hiv", "sars-cov-2"] | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v2 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
mamba-version: "*" | |
channels: conda-forge,bioconda,defaults | |
channel-priority: strict | |
activate-environment: V-pipe | |
auto-update-conda: true | |
- name: Install dependencies | |
run: mamba install --yes snakemake-minimal | |
- name: Setup project | |
run: | | |
mkdir -p /tmp/project/${{ matrix.virus }}/ | |
cd /tmp/project/${{ matrix.virus }}/ | |
$GITHUB_WORKSPACE/init_project.sh -n | |
- name: Run tests | |
working-directory: ./tests | |
run: ./regression_tests.sh ${{ matrix.virus }} | |
- name: Archive code coverage results | |
uses: actions/upload-artifact@v2 | |
with: | |
name: regression test output and diffs | |
path: | | |
/tmp/v-pipe_tests/* | |
if-no-files-found: ignore |