Skip to content

Modularize explore #244

Modularize explore

Modularize explore #244

Workflow file for this run

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