long_reads.yml

name: SPAdes long-read tests

on:
  workflow_dispatch:
  pull_request:
    paths-ignore:
      - 'docs/**'
      - 'mkdocs.yml'
  push:
    tags:
      - '*'
  schedule:
  - cron: '0 23 * * 1,4'


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

  ctg-ecoli-is220:
    name: 'Untrusted contigs E.coli is220'
    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/spades_tests/CTG_E.coli_is220.info

  ctg-geophsycobacter:
    name: 'Untrustred contigs Geophsycobacter'
    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/spades_tests/CTG_Geophsycobacter.info

  pb-amirum:
    name: 'PacBio A.mirum'
    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/spades_tests/PB_A.mirum.info

  pb-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/spades_tests/PB_M.ruber.info

  pb-mp-amirum:
    name: 'PacBio+Mate-pairs A.mirum'
    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/spades_tests/PB_MP_A.mirum.info

  pb-mp-mruber:
    name: 'PacBio+Mate-pairs 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/spades_tests/PB_MP_M.ruber.info

  pb-ecoli:
    name: 'PacBio P4 E.coli is200'
    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/spades_tests/PB_P4_E.coli_is220.info

  pb-pheparinus:
    name: 'PacBio P.heparinus'
    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/spades_tests/PB_P.heparinus.info

  tctg-kpneumoniae:
    name: 'Trusted contigs K.pneumoniae'
    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/spades_tests/TCTG_K.pneumoniae.info

  tctg-pstipitis:
    name: 'Trusted contigs P.stipitis'
    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/spades_tests/TCTG_P.stipitis.info

  tctg-ssmaragdinae:
    name: 'Trusted contigs S.smaragdinae quaked'
    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/spades_tests/TCTG_S.smaragdinae_quake.info