quantms/.github/workflows/extended_ci.yml at master · bigbio/quantms · GitHub

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name: nf-core extended CI
# This workflow runs the pipeline with all singularity or docker
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:
  test-docker:
    name: Docker Tests
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantms') }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "25.04.0"
          - "latest-everything"
        test_profile:
          [
            "test_lfq",
            "test_dia",
            "test_localize",
            "test_tmt",
            "test_dda_id_alphapeptdeep",
            "test_dda_id_fine_tuning",
            "test_dda_id_ms2pip",
            "test_tmt_corr",
          ]
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: ${{ matrix.test_profile }}
      EXEC_PROFILE: docker

    steps:
      - name: Checkout repository
        uses: actions/checkout@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 in docker profile
        if: 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 in docker profile (master branch)
        if: 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 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.NXF_VER }}_${{ github.run_id }}_${{ github.run_attempt }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false
          if-no-files-found: warn

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

  test-singularity:
    name: Singularity Tests
    needs: test-docker
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'bigbio/quantms') }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "25.04.0"
          - "latest-everything"
        test_profile:
          [
            "test_lfq",
            "test_dia",
            "test_localize",
            "test_tmt",
            "test_dda_id_ms2pip",
            "test_dda_id_alphapeptdeep",
            "test_tmt_corr",
            "test_dda_id_fine_tuning",
          ]
    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@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 in singularity profile
        if: 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 in singularity profile (master branch)
        if: 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 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"

      - name: Set timestamp
        run: |
          echo "ARTIFACT_TIMESTAMP=$(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 }}_${{ github.run_id }}_${{ github.run_attempt }}_${{ env.ARTIFACT_TIMESTAMP }}
          include-hidden-files: true
          path: failed_logs
          overwrite: false
          if-no-files-found: warn

      - uses: actions/upload-artifact@v4
        if: always()
        name: Upload results
        with:
          name: ${{ matrix.test_profile }}_${{ matrix.NXF_VER }}_${{ github.run_id }}_${{ github.run_attempt }}_${{ env.ARTIFACT_TIMESTAMP }}_results
          include-hidden-files: true
          path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
          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 }}_${{ github.run_id }}_${{ github.run_attempt }}_${{ env.ARTIFACT_TIMESTAMP }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false
          if-no-files-found: warn
# Conda tests removed - Conda is no longer supported