diann_private.yml

name: Fork-specific CI for test_latest_dia

# Trigger only for your fork and the 'test_latest_dia' test profile
on:
  push:
    branches:
      - dev
  pull_request:
    branches:
      - dev
    paths:
      - "**.yml"

env:
  NXF_ANSI_LOG: false

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true

jobs:
  test:
    name: Run test_latest_dia with Docker
    runs-on: ubuntu-latest
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: test_latest_dia
      EXEC_PROFILE: docker

    # Ensure this workflow only runs for your fork
    if: ${{ github.repository == 'ypriverol/quantms' }}

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "24.04.2" # Or the Nextflow version you prefer

      - name: Log in to GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ secrets.GHCR_USERNAME }}
          password: ${{ secrets.GHCR_TOKEN }}

      - name: Run test_latest_dia with Docker
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results

      - name: Gather failed logs
        if: failure() || cancelled()
        run: |
          mkdir failed_logs
          failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2)
          while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed"

      - uses: actions/upload-artifact@v4
        if: failure() || cancelled()
        name: Upload failed logs
        with:
          name: failed_logs_${{ matrix.test_profile }}_${{ matrix.exec_profile }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload results
        with:
          name: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
          include-hidden-files: true
          path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
          overwrite: false

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload log
        with:
          name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false