ci.yml

# https://github.com/actions/starter-workflows/blob/main/ci/python-package-conda.yml

name: ci

on:
  push:
    branches:
      - master
      - tests
    paths-ignore:
      - "README.md"
      - "docs/**"
  pull_request:
    branches:
      - master
  schedule:
    # * is a special character in YAML so you have to quote this string
    - cron: "3 14 15 * *"

jobs:
  build-and-test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
      max-parallel: 5

    steps:
      - uses: actions/checkout@v3
        with:
          ref: "master"
      - name: Set up Python 3.10
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Add Conda to system path
        run: |
          # $CONDA is an environment variable pointing to the root of the miniconda directory
          echo $CONDA
          echo $CONDA/bin >> $GITHUB_PATH
      - name: Install dependencies
        run: |
          conda env update --file environment.yml --name base
          conda install flake8 pytest pytest-cov
      - name: Lint with flake8
        run: |
          # stop the build if there are Python syntax errors or undefined names
          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
          flake8 . --count --exit-zero --max-complexity=30 \
          --max-line-length=127 --statistics
      - name: Test with pytest
        run: |
          python -m pytest
      - name: Generate coverage report
        run: |
          python -m pytest --cov=fba --cov-report=xml
      - name: Upload coverage report to Codecov
        uses: codecov/codecov-action@v1
        with:
          env_vars: OS,PYTHON
          name: codecov-umbrella
          fail_ci_if_error: true
          verbose: true
      - name: Install fba
        run: |
          pip install -e .
      - name: Inspect files
        run: |
          ls -l ${GITHUB_WORKSPACE}
          ls -l ${GITHUB_WORKSPACE}/fba
          ls -l ${GITHUB_WORKSPACE}/tests/
      - name: Test qc, extract, count, demultiplex
        run: |
          fba

          ls -l ${GITHUB_WORKSPACE}/tests/qc-extract-count-demultiplex
          cd ${GITHUB_WORKSPACE}/tests/qc-extract-count-demultiplex

          fba qc -1 read_R1.fq.gz -2 read_R2.fq.gz \
          -w cell_barcodes.tsv.gz -f feature_barcodes.tsv.bz2 \
          -t 2 -n 2000 --chunk_size 400 --output_directory test_qc

          fba extract -1 read_R1.fq.gz -2 read_R2.fq.gz \
          -w cell_barcodes.tsv.gz \
          -f feature_barcodes.tsv.bz2 \
          -o test_feature_barcoding_output.tsv.gz \
          --read1_coordinate 0,16 \
          --read2_coordinate 31,51 \
          -cb_m 2 -fb_m 1

          fba count -i test_feature_barcoding_output.tsv.gz \
          -o test_matrix_featurecount.csv.gz

          fba demultiplex -i matrix_featurecount.csv.gz \
          -q 0.75 -cm kmedoids -v -vm umap \
          --output_directory test_demultiplexed
      - name: Test map
        run: |
          ls -l ${GITHUB_WORKSPACE}/tests/map
          cd ${GITHUB_WORKSPACE}/tests/map

          # bwa
          fba map -1 read_R1.fq.gz -2 read_R2.fq.gz \
          -w cell_barcodes.tsv.gz \
          -f features.tsv.bz2 \
          -o test_matrix_featurecount.csv.gz \
          --read1_coordinate 0,16 \
          --output_directory test_barcode_mapping \
          --num_n_ref 0

          # bowtie2
          fba map -1 read_R1.fq.gz -2 read_R2.fq.gz \
          -w cell_barcodes.tsv.gz \
          -f features.tsv.bz2 \
          -o test_matrix_featurecount.csv.gz \
          --read1_coordinate 0,16 \
          -al bowtie2 \
          --mapq 10 \
          --output_directory test_barcode_mapping \
          --num_n_ref 0