ci.yml

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  push:
    branches:
      - dev
  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:
    env:
      NXF_ANSI_LOG: false
      CAPSULE_LOG: none
      TEST_PROFILE: ${{ matrix.test_profile }}
      EXEC_PROFILE: ${{ matrix.exec_profile }}

    name: Run pipeline with test data
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        # Nextflow versions
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
        test_profile:
          ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"]
        exec_profile: ["docker"]
        exclude:
          - test_profile: test_dia
            exec_profile: "conda"
          - test_profile: test_localize
            exec_profile: "conda"
          - NXF_VER: "latest-everything"
            exec_profile: "conda"
        include:
          - test_profile: test_lfq
            exec_profile: "conda"
          - test_profile: test_dda_id
            exec_profile: "conda"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

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

      - name: Set up Apptainer
        if: matrix.exec_profile == 'singularity'
        uses: eWaterCycle/setup-apptainer@main

      - name: Set up Singularity
        if: matrix.exec_profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - name: Install micromamba
        env:
          MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba
        if: matrix.exec_profile == 'conda'
        run: |
          wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
          echo "$(pwd)/bin" >> $GITHUB_PATH
          echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH
          ./bin/micromamba shell init -s bash
          echo $'channels:\n  - conda-forge\n  - bioconda\n  - defaults\nuse_lockfiles: false' >> ~/.mambarc

      - name: Install Singularity with defaults
        if: matrix.exec_profile == 'singularity'
        uses: singularityhub/install-singularity@main

      - name: Disk space cleanup
        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

      - name: Run pipeline with test data in docker/singularity profile
        if: matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity'
        # TODO nf-core: You can customise CI pipeline run tests as required
        # For example: adding multiple test runs with different parameters
        # Remember that you can parallelise this by using strategy.matrix
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results

      - name: Run pipeline with test data in conda profile (and single-threaded)
        env:
          MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba
        if: matrix.exec_profile == 'conda'
        # TODO nf-core: You can customise CI pipeline run tests as required
        # For example: adding multiple test runs with different parameters
        # Remember that you can parallelise this by using strategy.matrix
        run: |
          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --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 }}_${{ matrix.NXF_VER }}
          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 }}_${{ matrix.NXF_VER }}_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 }}_${{ matrix.NXF_VER }}.log
          include-hidden-files: true
          path: .nextflow.log
          overwrite: false