ci.yml

name: CI
# This workflow runs the pipeline with the minimal test dataset to check that
# it completes without any syntax errors
on:
  push:
    branches:
      - main
      - dev
  pull_request:
    branches:
      - main
      - dev
    draft: true

env:
  NXF_ANSI_LOG: false

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

jobs:
  test:
    name: Install and run self-test pipeline
    # Only run on push if this is in the main repository
    if: "${{ github.repository == 'genomic-medicine-sweden/gms_16s' }}"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "24.10.0"
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        # For running (locally) with ACT, we use a docker image with Nextflow pre-installed
        if: "${{ ! github.event.act }}"
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1

      - name: Install Singularity
        # For running (locally) with ACT, we use a docker image with Singularity already installed
        if: "${{ ! github.event.act }}"
        run: |
          wget https://github.com/apptainer/singularity/releases/download/v3.8.7/singularity-container_3.8.7_amd64.deb && sudo dpkg -i singularity-container_3.8.7_amd64.deb

      - name: Report disk-usage before make install
        run:
          df -h

      - name: Run Make install
        run:
          make install

      - name: Report disk-usage after make install
        run:
          df -h

          #- name: Run pipeline with test data
          #  run: |
          #    nextflow  \
          #      -log $(pwd)/nextflow.log \
          #      run main.nf \
          #      --outdir results \
          #      --db $(pwd)/assets/databases/emu_database \
          #      --seqtype map-ont \
          #       -profile singularity,test \
          #      --quality_filtering \
          #      --longread_qc_qualityfilter_minlength 1200 \
          #      --longread_qc_qualityfilter_maxlength 1800 \
          #      --merge_fastq_pass $(pwd)/assets/test_assets/ci; \

      - name: Run nf-test
        run: |
          nf-test test tests/main.nf.test