IsoQuant/.github/workflows/Barcode.Mouse.10x.FullWhitelist.yml at master · ablab/IsoQuant · GitHub

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name: Barcode Mouse 10x Full Whitelist

on:
  workflow_dispatch:
  schedule:
  - cron: '0 2 * * 6'

env:
  LAUNCHER: ${{github.workspace}}/isoquant_tests/github/run_barcode_test.py
  CFG_DIR: /abga/work/andreyp/ci_isoquant/data/barcodes
  BIN_PATH: /abga/work/andreyp/ci_isoquant/bin/
  OUTPUT_BASE: /abga/work/andreyp/ci_isoquant/output/${{github.ref_name}}/barcodes/

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

jobs:
  check-changes:
    runs-on:
      labels: [isoquant]
    name: 'Check for recent changes'
    outputs:
      has_changes: ${{steps.check.outputs.has_changes}}
    steps:
      - name: 'Checkout'
        uses: actions/checkout@v3
        with:
          fetch-depth: 0

      - name: 'Check for commits in last 7 days'
        id: check
        run: |
          # Always run on manual trigger
          if [ "${{github.event_name}}" = "workflow_dispatch" ]; then
            echo "has_changes=true" >> $GITHUB_OUTPUT
            exit 0
          fi
          # Check for commits in last 7 days
          COMMITS=$(git log --oneline --since="7 days ago" | wc -l)
          if [ "$COMMITS" -gt 0 ]; then
            echo "Found $COMMITS commits in last 7 days"
            echo "has_changes=true" >> $GITHUB_OUTPUT
          else
            echo "No commits in last 7 days, skipping"
            echo "has_changes=false" >> $GITHUB_OUTPUT
          fi

  launch-runner:
    needs: check-changes
    if: needs.check-changes.outputs.has_changes == 'true'
    runs-on:
      labels: [isoquant]
    name: 'Running barcode detection QC'

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

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

      - name: 'Mouse 10x v3 3M full whitelist'
        if: always()
        shell: bash
        env:
          STEP_NAME: Mouse.10x.v3.3M.full
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.yaml -o ${{env.OUTPUT_BASE}}

      - name: 'Mouse 10x v2 737K full whitelist'
        shell: bash
        if: always()
        env:
          STEP_NAME: Mouse.10x.v2.737K.full
        run: |
          export PATH=$PATH:${{env.BIN_PATH}}
          python3 ${{env.LAUNCHER}} ${{env.CFG_DIR}}/${{env.STEP_NAME}}.yaml -o ${{env.OUTPUT_BASE}}