python-package-conda.yml

name: Combined Workflow

on:
  # Runs on pushes targeting the default branch
  push:
    branches: ["master"]
  pull_request:
    branches: ["master"]
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

defaults:
  run:
    shell: bash -el {0} # use default shell

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  build-and-dryrun:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 1

    steps:
      - name: Checkout
        uses: actions/checkout@v3.5.2

      # - name: Get current month
      #   id: date
      #   run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}"

      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          # persist on the same month.
          cache-environment-key: atlasenv- #${{ steps.date.outputs.date }}

      - name: Install atlas
        run: |
          python -m pip install . --no-deps -vv

      - name: Test atlas
        run: |
          atlas --help
          atlas --version

      - name: test import modules atlas
        run: |
          python -c "from atlas import utils"

      - name: Dryrun
        run: test/dryrun.sh

  run-qc-and-assembly:
    runs-on: ubuntu-latest
    needs: build-and-dryrun
    env:
      N_THREADS: 2
      MEM: 0.8

    steps:
      - name: Checkout
        uses: actions/checkout@v3.5.2

      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          cache-environment-key: atlasenv-

      - name: Install atlas
        run: |
          python -m pip install . --no-deps -vv
          atlas --help

      - name: get example data
        id: get-data
        uses: actions/cache/restore@v3
        with:
          path: test_reads.tar.gz
          key: example-data

      - name: Download test data
        if: steps.get-data.outputs.cache-hit != 'true'
        run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz

      - name: cache example data
        if: steps.get-data.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: test_reads.tar.gz
          key: ${{ steps.get-data.outputs.cache-primary-key }}

      - name: extract data
        run: |
          tar -xzf test_reads.tar.gz 
          ls -l test_reads

      - name: get conda envs
        id: get-envs
        uses: actions/cache/restore@v3
        with:
          path: databases
          key: conda-envs-assembly

        # - name: upack conda envs
        #   if: steps.get-envs.outputs.cache-hit != 'true'
        #   run: tar -xzf assembly_conda_envs.tar.gz

      - name: Init
        run: |
          atlas init "test_reads" --threads "$N_THREADS" --working-dir wd

      - name: Install dependencies for qc and assembly
        if: steps.get-envs.outputs.cache-hit != 'true'
        run: atlas run assembly --conda-create-envs-only -w wd

      - name: List envs
        run: ls -l databases/conda_envs

      - name: Store conda envs
        if: steps.get-envs.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: databases
          key: ${{ steps.get-envs.outputs.cache-primary-key }}

      - name: Run QC
        run: |
          atlas run qc --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

      - name: Test Assembly
        run: |
          atlas run assembly --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd

      - name: Store Logs
        uses: actions/upload-artifact@v3
        with:
          name: logs
          path: wd/logs

      - name: Store Sample Logs
        uses: actions/upload-artifact@v3
        with:
          name: sample_logs
          path: wd/sample1/logs

      - name: Store reports
        uses: actions/upload-artifact@v3
        with:
          name: reports
          path: wd/reports

      - name: Cache working dir
        uses: actions/cache/save@v3
        with:
          path: wd
          key: assembly-working-dir

  run-genecatalog:
    runs-on: ubuntu-latest
    needs: [build-and-dryrun, run-qc-and-assembly]
    env:
      N_THREADS: 2
      MEM: 3

    steps:
      - name: Checkout
        uses: actions/checkout@v3.5.2

      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          cache-environment-key: atlasenv-

      - name: install atlas
        run: |
          python -m pip install . --no-deps -vv
          atlas --help

      - name: get conda envs
        id: get-envs
        uses: actions/cache/restore@v3
        with:
          path: databases
          key: conda-envs-genecatalog
          restore-keys: |
            conda-envs-assembly
            conda-envs-

      - name: Restore working dir
        uses: actions/cache/restore@v3
        with:
          path: wd
          key: assembly-working-dir

      - name: dryrun assembly shold need nothing to be done
        run: |
          ls -l wd
          ls -l databases/conda_envs
          atlas run assembly -w wd -n

      - name: test Genecatalog
        run: |
          atlas run genecatalog --restart-times=2 --working-dir wd --omit-from combine_egg_nogg_annotations combine_dram_genecatalog_annotations

      - name: Store Logs
        uses: actions/upload-artifact@v3
        with:
          name: logs
          path: wd/logs

      - name: Store Sample Logs
        uses: actions/upload-artifact@v3
        with:
          name: sample_logs
          path: wd/sample1/logs

      - name: Store conda envs
        #if: steps.get-envs.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: databases
          key: ${{ steps.get-envs.outputs.cache-primary-key }}

  run-binning:
    runs-on: ubuntu-latest
    needs: [build-and-dryrun, run-qc-and-assembly]
    env:
      MEM: 0.9

    steps:
      - name: Checkout
        uses: actions/checkout@v3.5.2

      - uses: mamba-org/setup-micromamba@v1
        with:
          environment-file: atlasenv.yml
          environment-name: atlasenv
          cache-environment-key: atlasenv-

      - name: install atlas
        run: |
          python -m pip install . --no-deps -vv
          atlas --help

      - name: get conda envs
        id: get-envs
        uses: actions/cache/restore@v3
        with:
          path: databases
          key: conda-envs-binning
          restore-keys: |
            conda-envs-

      - name: Restore working dir
        uses: actions/cache/restore@v3
        with:
          path: wd
          fail-on-cache-miss: true
          key: assembly-working-dir

      - name: dryrun assembly shold need nothing to be done
        run: |
          ls -l wd
          ls -l databases
          ls -l databases/conda_envs
          atlas run assembly -w wd -n

      - name: test binning
        run: |
          atlas run binning --restart-times=2 --working-dir wd --omit-from checkm2_download_db --max-mem $MEM &> >(tee wd/logs/atlas_binning.log)

      - name: Store Logs
        uses: actions/upload-artifact@v3
        with:
          name: logs_binning
          path: wd/logs

      - name: Store Sample Logs
        uses: actions/upload-artifact@v3
        with:
          name: sample_logs_binning
          path: wd/sample1/logs

      - name: Store conda envs
        # if: steps.get-envs.outputs.cache-hit != 'true'
        uses: actions/cache/save@v3
        with:
          path: databases
          key: ${{ steps.get-envs.outputs.cache-primary-key }}

  # run-quantify-genomes:
  #   runs-on: ubuntu-latest
  #   needs: build-and-dryrun

  #   steps:
  #     - name: Checkout
  #       uses: actions/checkout@v3.5.2

  #     - uses: mamba-org/setup-micromamba@v1
  #       with:
  #         environment-file: atlasenv.yml
  #         environment-name: atlasenv
  #         cache-environment-key: atlasenv-

  #     - name: Install atlas
  #       run: |
  #         python -m pip install . --no-deps -vv
  #         atlas --help

  #     - name: get conda envs
  #       id: get-envs
  #       uses: actions/cache/restore@v3
  #       with:
  #         path: databases
  #         key: conda-envs-assembly
  #         restore-keys: conda-envs-*