usecases.yml

name: SPAdes usecases

on:
  workflow_dispatch:
  push:
    branches:
      - master
      - main
      - next
    tags:
      - '*'
    paths-ignore:
      - 'docs/**'
      - 'mkdocs.yml'
  pull_request:
    paths-ignore:
      - 'docs/**'
      - 'mkdocs.yml'

env:
  BUILD_TYPE: Release
  BUILD_DIR: ${{github.workspace}}/build
  INSTALL_DIR: ${{github.workspace}}/spades
  SRC_DIR: ${{github.workspace}}/src
  PKG: SPAdes-*-Linux

jobs:
  build:
    runs-on: self-hosted
    name: '🚧 Build SPAdes'

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1

      - name: '⚙️ Install ccache'
        uses: hendrikmuhs/ccache-action@v1.2
        with:
          variant: sccache
          key: sccache-${{env.BUILD_TYPE}}

      - name: '⚙️ Configure CMake'
        run: >
          cmake
          -B ${{env.BUILD_DIR}}
          -S ${{env.SRC_DIR}}
          -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
          -DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}

      - name: '🚧 Build'
        run: >
          cmake
          --build ${{env.BUILD_DIR}}
          -j16
          -t package

      - name: '📦 Package'
        uses: actions/upload-artifact@v4
        with:
          name: build-artifacts
          path: |
            ${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

  mc-bcereus-truseq-100x:
    name: 'Multicell B.cereus TruSeq 100x'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Multicell_B.cereus_TruSeq_100x.info

  nextera-lmonocytogenes:
    name: 'Nextera L.monocytogenes'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Nextera_L.monocytogenes.info

  contigs-ecoli-jgi-lane7:
    name: 'Contigs E.coli JGI lane 7'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Contigs_E.coli_JGI_lane7.info

  fullrun-mruber-jgi-lane9:
    name: 'Full run M.ruber JGI lane 9'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Full_run_M.ruber_JGI_lane9_prenormalized.info

  iontorrnent-ecoli-k12:
    name: 'IonTorrent E.coli K12'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/IonTorrent_E.coli_K12.info

  mate-pair-bfaecium:
    name: 'Mate-pairs B.faecium'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Mate-pairs_B.faecium.info

  sc-pheparinus-jgi-lane7:
    name: 'Single-cell P.heparinus JGI lane 7'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Single-cell_P.heparinus_JGI_lane7_prenormalized.info

  plasmid-ccallunae:
    name: 'plasmidSPAdes C.callunae'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/plasmidSPAdes_C.callunae.info

  single-reads-ecoli-deeptrench:
    name: 'Single reads E.coli Deeptrench'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Single_reads_E.coli_deeptrench.info

  pacbio-mruber:
    name: 'PacBio M.ruber'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/PacBio_M.ruber.info

  saves-ecoli-100k:
    name: 'Saves E.coli 100K'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Saves_E.coli_100K.info

  saves-ecoli-ucsd-lane1:
    name: 'Saves E.coli UCSD lane 1'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/Saves_E.coli_UCSD_lane1.info

  metaspades-jgi-150:
    name: 'metaSPAdes JGI 150'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/metaSPAdes_JGI_150.info

  metaviral-test:
    name: 'metaviralSPAdes ERR525599'
    runs-on: self-hosted
    needs: build

    steps:
      - name: '🧹 Cleanup'
        run: >
          set -e &&
          shopt -s dotglob &&
          rm -rf *

      - name: '🧰 Checkout'
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
      - name: '📦 Download package'
        uses: actions/download-artifact@v4
        with:
          name: build-artifacts
          path: ${{env.INSTALL_DIR}}
      - name: '📦 Unpack package'
        working-directory: ${{env.INSTALL_DIR}}
        run: >
          tar -zxf ${{env.PKG}}.tar.gz
      - name: 'Assembly'
        run: >
          ${{env.SRC_DIR}}/test/teamcity/github_runner.py
          --spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
          --no_contig_archive
          /data/pipeline_tests/metaviral_test.info