extended_ci.yml

name: nf-core extended CI
# Job dependency chain:
#   test-default (1.8.1, fast, public) → test-latest (2.2.0, all features)
#                                      → test-singularity (1.8.1, Singularity)
# If test-default fails, downstream jobs are skipped to save resources.
on:
  push:
    branches:
      - dev
      - master
  pull_request:
  release:
    types: [published]
  workflow_dispatch:

env:
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

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

jobs:
  # ──────────────────────────────────────────────────────────────────────────
  # Stage 1: Default tests — DIA-NN 1.8.1 (public, fast, no auth)
  #           Must pass before any other job runs.
  # ──────────────────────────────────────────────────────────────────────────
  test-default:
    name: "Default [${{ matrix.test_profile }}] DIA-NN=1.8.1 NXF=${{ matrix.NXF_VER }}"
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantmsdiann') }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: true
      matrix:
        NXF_VER: ["25.10.4", "latest-everything"]
        test_profile: ["test_dia", "test_dia_dotd"]
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: ${{ matrix.test_profile }}
      EXEC_PROFILE: docker

    steps:
      - name: Checkout repository
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - name: Set up Java 17
        uses: actions/setup-java@v4
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@v1.3.1

      - name: Run pipeline with test data
        if: github.ref != 'refs/heads/master' && github.event.pull_request.base.ref != 'master'
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,dev --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results

      - name: Run pipeline with test data (master branch)
        if: github.ref == 'refs/heads/master' || github.event.pull_request.base.ref == 'master'
        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 -p failed_logs
          if [ -f "${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt" ]; then
            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"
          fi

      - name: Set timestamp
        if: always()
        run: echo "TS=$(date +%s)" >> $GITHUB_ENV

      - uses: actions/upload-artifact@v4
        if: failure() || cancelled()
        name: Upload failed logs
        with:
          name: failed_logs_${{ matrix.test_profile }}_${{ matrix.NXF_VER }}_${{ env.TS }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false
          if-no-files-found: warn

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload log
        with:
          name: nextflow_${{ matrix.test_profile }}_${{ matrix.NXF_VER }}_${{ env.TS }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false
          if-no-files-found: warn

  # ──────────────────────────────────────────────────────────────────────────
  # Stage 2a: Latest DIA-NN (2.2.0) — all features
  #           Only runs after test-default passes.
  # ──────────────────────────────────────────────────────────────────────────
  test-latest:
    name: "Latest [${{ matrix.test_profile }}] DIA-NN=2.2.0"
    needs: test-default
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        test_profile:
          [
            "test_latest_dia",
            "test_dia_quantums",
            "test_dia_parquet",
            "test_dia_qpx",
            "test_dda",
            "test_dia_skip_preanalysis",
          ]
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: ${{ matrix.test_profile }}
      EXEC_PROFILE: docker

    steps:
      - name: Checkout repository
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - name: Set up Java 17
        uses: actions/setup-java@v4
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "25.10.4"

      - name: Log in to GitHub Container Registry
        env:
          GHCR_TOKEN: ${{ secrets.GHCR_TOKEN }}
        if: env.GHCR_TOKEN != ''
        run: |
          echo "${{ secrets.GHCR_TOKEN }}" | docker login ghcr.io -u ${{ secrets.GHCR_USERNAME }} --password-stdin

      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@v1.3.1

      - name: Run pipeline with test data
        if: github.ref != 'refs/heads/master' && github.event.pull_request.base.ref != 'master'
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,dev --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results

      - name: Run pipeline with test data (master branch)
        if: github.ref == 'refs/heads/master' || github.event.pull_request.base.ref == 'master'
        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 -p failed_logs
          if [ -f "${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt" ]; then
            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"
          fi

      - name: Set timestamp
        if: always()
        run: echo "TS=$(date +%s)" >> $GITHUB_ENV

      - uses: actions/upload-artifact@v4
        if: failure() || cancelled()
        name: Upload failed logs
        with:
          name: failed_logs_latest_${{ matrix.test_profile }}_${{ env.TS }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false
          if-no-files-found: warn

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload log
        with:
          name: nextflow_latest_${{ matrix.test_profile }}_${{ env.TS }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false
          if-no-files-found: warn

  # ──────────────────────────────────────────────────────────────────────────
  # Stage 2b: Singularity — default tests only (public containers)
  #           Only runs after test-default passes.
  # ──────────────────────────────────────────────────────────────────────────
  test-singularity:
    name: "Singularity [${{ matrix.test_profile }}] DIA-NN=1.8.1 NXF=${{ matrix.NXF_VER }}"
    needs: test-default
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantmsdiann') }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER: ["25.10.4", "latest-everything"]
        test_profile: ["test_dia", "test_dia_dotd"]
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: ${{ matrix.test_profile }}
      EXEC_PROFILE: singularity
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
        with:
          fetch-depth: 0

      - uses: actions/setup-java@v4
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Set up Singularity
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Install Singularity with defaults
        uses: singularityhub/install-singularity@main

      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@v1.3.1

      - name: Run pipeline with test data
        if: github.ref != 'refs/heads/master' && github.event.pull_request.base.ref != 'master'
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,dev --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results

      - name: Run pipeline with test data (master branch)
        if: github.ref == 'refs/heads/master' || github.event.pull_request.base.ref == 'master'
        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 -p failed_logs
          if [ -f "${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt" ]; then
            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"
          fi

      - name: Set timestamp
        if: always()
        run: echo "TS=$(date +%s)" >> $GITHUB_ENV

      - uses: actions/upload-artifact@v4
        if: failure() || cancelled()
        name: Upload failed logs
        with:
          name: failed_logs_sing_${{ matrix.test_profile }}_${{ matrix.NXF_VER }}_${{ env.TS }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false
          if-no-files-found: warn

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload log
        with:
          name: nextflow_sing_${{ matrix.test_profile }}_${{ matrix.NXF_VER }}_${{ env.TS }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false
          if-no-files-found: warn