adding samtools view -F 4; closes #46 #30
Workflow file for this run
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name: Test build koverage envs | |
on: | |
push: | |
branches: [ "main" ] | |
paths: | |
- '.github/workflows/build-koverage-envs.yaml' | |
- 'config/**' | |
- 'tests/**' | |
- 'test_data/**' | |
- 'workflow/**' | |
- 'koverage/**' | |
- 'setup.py' | |
pull_request: | |
branches: [ "main" ] | |
paths: | |
- '.github/workflows/build-koverage-envs.yaml' | |
- 'config/**' | |
- 'tests/**' | |
- 'test_data/**' | |
- 'workflow/**' | |
- 'koverage/**' | |
- 'setup.py' | |
permissions: | |
contents: read | |
jobs: | |
tests: | |
name: "Kov envs for Python ${{ matrix.python-version }} on ${{ matrix.os }}" | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -el {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest] | |
python-version: ["3.11"] | |
steps: | |
- uses: "actions/checkout@v3" | |
with: | |
fetch-depth: 0 | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
auto-update-conda: true | |
miniforge-version: "latest" | |
miniforge-variant: Mambaforge | |
use-mamba: true | |
mamba-version: "*" | |
channels: conda-forge,bioconda,defaults | |
channel-priority: strict | |
python-version: ${{ matrix.python-version }} | |
auto-activate-base: false | |
- name: "Test build koverage and build kov envs on ${{ matrix.os }} for Python ${{ matrix.python-version }}" | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install . | |
koverage test build_envs |