python-app.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python application

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: set up python
        uses: actions/setup-python@v2
        with:
          python-version: "3.8.10"
      - name: install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install flake8 pytest
          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
      - 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=10 --max-line-length=127 --statistics
      - name: test gen_reads
        run: python gen_reads_runner.py -R 101 -o test -r data/H1N1.fasta
      
  job-valBAM:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v2
      - name: Execute validateBAM.py
        run: |
          cd ${{ github.workspace }}/utilities
          python validateBam.py ../data/baby.bam
      - run: echo "🍏 This job's status is ${{ job.status }}." 
  
  job-valFQ:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v2
      - name: Execute validateFQ.py
        run: |
           pip install biopython
           cd ${{ github.workspace }}/utilities
           python validateFQ.py ../data/baby.fastq
      - run: echo "🍏 This job's status is ${{ job.status }}." 
      
#   job-computegc:
#     runs-on: ubuntu-latest
#     steps:
#        - name: Check out repository code
#          uses: actions/checkout@v2
#        - name: Execute compute_gc.py
#          run: |
#            pip install numpy
#            pip install biopython
#            pip install pandas
#            cd ${{ github.workspace }}/utilities
#            python compute_gc.py -i ../data/small.genomecov -r ../data/ecoli.fa -o gcop
#        - run: echo "🍏 This job's status is ${{ job.status }}."