Modularize explore #244
Workflow file for this run
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name: Anglerfish | |
on: [push, pull_request] | |
jobs: | |
run_anglerfish: | |
name: Anglerfish py-${{ matrix.python-version }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: [3.12] | |
steps: | |
# Checkout code and install miniconda + environment | |
- uses: actions/checkout@v4 | |
- uses: mamba-org/setup-micromamba@v1 | |
with: | |
init-shell: bash | |
create-args: >- | |
python=${{ matrix.python-version }} | |
pip | |
environment-file: environment.yml | |
environment-name: anglerfish-dev | |
# Install Anglerfish | |
- shell: bash -l {0} | |
name: Install Anglerfish | |
run: | | |
python -m pip install . | |
# Run anglerfish --help | |
- shell: bash -l {0} | |
name: Test anglerfish | |
run: | | |
anglerfish --help | |
# Run anglerfish using test data | |
- shell: bash -l {0} | |
name: Run anglerfish with test data | |
run: | | |
anglerfish run -s testdata/samples.csv | |
# Run anglerfish explore | |
- shell: bash -l {0} | |
name: Run anglerfish explore | |
run: | | |
anglerfish explore -f testdata/BC18_P14351_1001.fastq.gz -o explore_output |