snakemake_avamb.yml

# This workflow will install snakemake and AVAMB dependencies and run the AVAMB snakemake pipeline

name: AVAMB snakemake - runs daily

on:
  workflow_dispatch:
    inputs:
  schedule:
    - cron: "0 1 * * *"

permissions:
  contents: read

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.9"]

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v3
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip'
        cache-dependency-path: '**/pyproject.toml'
    - uses: mamba-org/setup-micromamba@v1
      with:
        micromamba-version: '1.3.1-0'
        environment-file: workflow_avamb/envs/avamb.yaml
        environment-name: avamb
        create-args: >-
          python=3.9.16
        init-shell: >-
          bash
        cache-environment: true
        post-cleanup: 'all'
    - name: Install dependencies to avamb environment
      run: |
        which pip
        pip install -e .
        pip freeze
        git clone https://github.com/chklovski/CheckM2.git 
      shell: micromamba-shell {0}
    - name: Install CheckM2 environment
      run: |
        micromamba create -n checkm2 python=3.8.15 pandas=2.1.1
        micromamba env update -n checkm2 --file workflow_avamb/envs/checkm2.yml
        eval "$(micromamba shell hook --shell=bash)"
        micromamba activate checkm2
        cd CheckM2  && git checkout e563159 && python setup.py install && cd ..
        checkm2 database --download
      shell: micromamba-shell {0}
    - name: Download fixtures
      run: |
        wget https://www.dropbox.com/scl/fi/q54wfho3ultb0otq5z3rh/testset_snakemake.zip\?rlkey\=7tbsc2giff0s42ppdmeb706fa\&dl\=0 -O testset_snakemake.zip
        unzip testset_snakemake.zip
        ls -la
        ls -la testset_snakemake
        pwd
    - name: Snakemake
      uses: snakemake/snakemake-github-action@v1.25.1
      with:
        directory: '.test'
        snakefile: 'workflow_avamb/avamb.snake.conda.smk'
        args: '--cores 4 --configfile workflow_avamb/config.json --use-conda'