IsoQuant/.github/workflows/Group_tests.yml at 8b912a942e1e12889ea7d920339bc1148414a41d · ablab/IsoQuant · GitHub

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name: Read grouping tests

on:
  workflow_dispatch:
  schedule:
  - cron: '0 2 * * 0,4'

env:
  RUN_NAME: Resume_tests
  LAUNCHER: ${{github.workspace}}/tests/github/run_pipeline.py
  CFG_DIR: /abga/work/andreyp/ci_isoquant/data
  BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
  OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/

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

jobs:
  launch-runner:
    runs-on:
      labels: [isoquant]
    name: 'Running IsoQuant and QC'

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

      - name: 'Checkout'
        uses: actions/checkout@v3
        with:
          fetch-depth: 1

      - name: 'Grouping by BAM tag'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP1.TAG.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Grouping by TSV file'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP2.TSV.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Grouping by read id'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP3.READID.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Grouping by file name'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP4.FILES.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Grouping by CSV file'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP5.CSV.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Default output with 7 groups'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP6.MTX.SIRVs
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Default output with 7 groups'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP6.MTX.SIRVs
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Specific TPM conversion with 7 groups'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP7.MTX_TPM.SIRVs
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Specific TPM conversion with all formats, 7 groups'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP8.MTX_FORMATS.SIRVs
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Default TPM conversion with all formats, 7 groups'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP9.MTX2.SIRVs
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Mixed groups for simulated SIRVs'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP10.MIX.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Mixed groups with duplicates for simulated SIRVs'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP11.MIX.WARN.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Barcode groups for simulated SIRVs'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP12.SC.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}

      - name: 'Barcode groups with multiple columns for simulated SIRVs'
        if: always()
        shell: bash
        env:
          STEP_NAME: GROUP13.SC.SIRVs.R10
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.cfg -o ${{env.OUTPUT_BASE}}