test_pipeline.yml

name: Test QCD Pipeline
run-name: ${{ github.actor }} is testing snakemake workflow 🚀
on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  Test-QCD-Pipeline:
    runs-on: ubuntu-latest
    steps:
      # - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
      # - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
      # - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
      
      - name: Checkout repository
        uses: actions/checkout@v3
      - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
      - run: echo "🖥️ The workflow is now ready to test your code on the runner."

      - name: List files in the repository
        run: |
          ls
      
      - name: Get working directory
        run: |
          pwd
      - name: Set up Miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: '3.10'
          auto-update-conda: true
          activate-environment: 'qcd_env_test'
          environment-file: 'qcd_environment.yaml'
          use-channel-priority: true
      
      - name: Install pip dependencies
        run: |
          source $CONDA/bin/activate
          conda activate qcd_env_test
          pip install --requirement .test/requirements.txt
          pip install dropbox
          pip install --upgrade tabulate
          pip install --upgrade snakemake
        
      # - name: Install singularity
      #   run: |
      #     sudo apt-get install -y \
      #      autoconf \
      #      automake \
      #      cryptsetup \
      #      fuse \
      #      fuse2fs \
      #      git \
      #      libfuse-dev \
      #      libglib2.0-dev \
      #      libseccomp-dev \
      #      libtool \
      #      pkg-config \
      #      runc \
      #      squashfs-tools \
      #      squashfs-tools-ng \
      #      uidmap \
      #      wget \
      #      zlib1g-dev 
      
      # - name: SSh into Actions
      #   uses: actions/checkout@v4
      # - name: Setup tmate session
      #   uses: mxschmitt/action-tmate@v3
      
           # ./mconfig --without-suid && \
           # make -C ./builddir && \
           # make -C ./builddir install
      - name: Install singularity
        uses: eWaterCycle/setup-singularity@v7
        with:
          singularity-version: 3.8.3
      # - name: Export Singularity Path
      #   run: |
      #     export PATH=/home/runner/go/src/github.com/hpcng/singularity-3.8.3/prefix/bin:$PATH
      #     echo "Singularity binary: $(which singularity)"
      #     singularity --version

      # # Diagnostic steps for Singularity capabilities 
      # - name: Install dependencies for Singularity
      #   run: |
      #     sudo apt-get update
      #     sudo apt-get install squashfuse fuse2fs gocryptfs

      # - name: Set up sysctl for unprivileged user namespaces
      #   run: |
      #     sudo sh -c 'echo kernel.unprivileged_userns_clone=1 > /etc/sysctl.d/90-unprivileged_userns.conf'
      #     sudo sysctl -p /etc/sysctl.d/90-unprivileged_userns.conf
      #     sudo sysctl --system
      #     uname -r
      #     sudo sh -c 'cat /proc/sys/kernel/unprivileged_userns_clone'
      #     sudo sh -c 'ls /etc/sysctl.d/90-unprivileged_userns.conf'

      # - name: Verify Singularity capabilities
      #   run: |
      #     singularity build --sandbox ubuntu_sandbox docker://ubuntu:20.04
      #     singularity exec --userns ubuntu_sandbox uname -a
      #     singularity exec --userns ubuntu_sandbox cat /proc/sys/kernel/unprivileged_userns_clone
      
      # # Debugging step: Print environment variables 
      # - name: Print environment variables
      #   run: printenv

      # Download FASTQ files from Dropbox
      - name: Download FASTQ files from Dropbox and copy it to local path
        env:
          DROPBOX_ACCESS_TOKEN: ${{ secrets.DROPBOX_ACCESS_TOKEN }}
        run: |
          source $CONDA/bin/activate
          conda activate qcd_env_test
          export DROPBOX_ACCESS_TOKEN=${DROPBOX_ACCESS_TOKEN}
          python3 download_fastqs.py
      # - name: SSh into Actions
      #   uses: actions/checkout@v4
      # - name: Setup tmate session
      #   uses: mxschmitt/action-tmate@v3
      
      - name: Create necessary directories
        run: |
          mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/quality_raw
          mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/trimmomatic
          mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/raw_coverage
          mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/spades
          
      # - name: SSh into Actions
      #   uses: actions/checkout@v4
      # - name: Setup tmate session
      #   uses: mxschmitt/action-tmate@v3

      - name: Snakemake workflow
        # run: |
        #   source $CONDA/bin/activate
        #   conda activate qcd_env_test
        #   snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 4 
        uses: snakemake/snakemake-github-action@v1.25.1
        with:
          directory: '.'
          snakefile: 'QCD.smk'
          # stagein: ./mconfig --without-suid && \
          #         make -C ./builddir && \
          #         make -C ./builddir install
          task: 'containerize'
          args: '--cores 4 --use-conda --use-singularity --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000' 
        #run: echo "🍏 This job's status is ${{ job.status }}."