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:
      - dev
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false
  # URLs to Influenza ref data should be updated in step with nextflow.config
  # default ncbi_influenza_fasta and ncbi_influenza_metadata params
  FASTA_ZST_URL: https://api.figshare.com/v2/file/download/41415330
  CSV_ZST_URL: https://api.figshare.com/v2/file/download/41415333

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

jobs:
  test_illumina:
    name: Run Illumina test
    # Only run on push if this is the nf-flu dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CFIA-NCFAD/nf-flu') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ['22.10.1', '24.04.2']
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4
      - name: Cache Nextflow binary
        uses: actions/cache@v4
        id: cache-nextflow
        with:
          path: /usr/local/bin/nextflow
          key: nextflow-${{ matrix.nxf_ver }}
      - name: Install Nextflow
        if: steps.cache-nextflow.outputs.cache-hit != 'true'
        env:
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Cache seqtk binary
        uses: actions/cache@v4
        id: cache-seqtk
        with:
          path: /usr/local/bin/seqtk
          key: seqtk
      - name: Build and install seqtk
        if: steps.cache-seqtk.outputs.cache-hit != 'true'
        run: |
          git clone --depth=1 https://github.com/lh3/seqtk.git
          cd seqtk
          make -j2
          make install
          which seqtk
      - name: Cache subsampled influenza.fna
        uses: actions/cache@v4
        id: cache-influenza-fna
        with:
          path: influenza-10k.fna.zst
          key: influenza-fna
      - name: Subsample NCBI influenza.fna
        if: steps.cache-influenza-fna.outputs.cache-hit != 'true'
        run: |
          curl --silent -SLk ${FASTA_ZST_URL} | zstdcat | seqtk sample -s 789 - 10000 | zstd -ck > influenza-10k.fna.zst
      - name: Cache influenza.csv
        uses: actions/cache@v4
        id: cache-influenza-csv
        with:
          path: influenza.csv.zst
          key: influenza-csv
      - name: Download influenza.csv
        if: steps.cache-influenza-csv.outputs.cache-hit != 'true'
        run: |
          curl --silent -SLk ${CSV_ZST_URL} > influenza.csv.zst
      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} \
            -profile test_illumina,docker \
            --ncbi_influenza_fasta influenza-10k.fna.zst \
            --ncbi_influenza_metadata influenza.csv.zst
      - name: Upload Artifact
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: illumina-test-results-${{ matrix.nxf_ver }}
          path: results/pipeline_info
      - name: Upload .nextflow.log
        uses: actions/upload-artifact@v4
        with:
          name: nextflow-log-illumina-${{ matrix.nxf_ver }}
          path: .nextflow.log

  test_nanopore:
    name: Run Nanopore test
    # Only run on push if this is the nf-flu dev branch (merged PRs)
    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'CFIA-NCFAD/nf-flu') }}
    runs-on: ubuntu-latest
    env:
      NXF_VER: ${{ matrix.nxf_ver }}
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        # Nextflow versions: check pipeline minimum and current latest
        nxf_ver: ['22.10.1', '24.04.2']
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4
      - name: Cache Nextflow binary
        uses: actions/cache@v4
        id: cache-nextflow
        with:
          path: /usr/local/bin/nextflow
          key: nextflow-${{ matrix.nxf_ver }}
      - name: Install Nextflow
        if: steps.cache-nextflow.outputs.cache-hit != 'true'
        env:
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/
      - name: Cache seqtk binary
        uses: actions/cache@v4
        id: cache-seqtk
        with:
          path: /usr/local/bin/seqtk
          key: seqtk
      - name: Build and install seqtk
        if: steps.cache-seqtk.outputs.cache-hit != 'true'
        run: |
          git clone --depth=1 https://github.com/lh3/seqtk.git
          cd seqtk
          make -j2
          make install
          which seqtk
      - name: Cache test sample reads
        uses: actions/cache@v4
        id: cache-reads
        with:
          path: reads/
          key: reads
      - name: Fetch IAV and IBV test seq
        if: steps.cache-reads.outputs.cache-hit != 'true'
        run: |
          mkdir -p reads/{run1,run2}
          # IBV test data
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/SRR24826962.sampled.fastq.gz > reads/SRR24826962.fastq.gz
          # IAV test data
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ERR6359501-10k.fastq.gz > reads/ERR6359501-10k.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run1-s11-ERR6359501.fastq.gz > reads/run1/s11-ERR6359501.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run1-s1-ERR6359501.fastq.gz > reads/run1/s1-ERR6359501.fastq.gz
          # uncompressed FASTQ should work too
          gunzip reads/run1/s1-ERR6359501.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run2-s22-ERR6359501.fastq.gz > reads/run2/s22-ERR6359501.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run2-s2-ERR6359501.fastq.gz > reads/run2/s2-ERR6359501.fastq.gz
          # neg ctrl 
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc15.fastq.gz > reads/ntc-bc15.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc31.fastq.gz > reads/ntc-bc31.fastq.gz
          curl -SLk --silent https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc47.fastq.gz > reads/ntc-bc47.fastq.gz
      - name: Prepare samplesheet.csv
        run: |
          echo "sample,reads" | tee -a samplesheet.csv
          echo "ERR6359501-10k,$(realpath reads/ERR6359501-10k.fastq.gz)" | tee -a samplesheet.csv
          echo "ERR6359501,$(realpath reads/run1)" | tee -a samplesheet.csv
          echo "ERR6359501,$(realpath reads/run2)" | tee -a samplesheet.csv
          echo "SRR24826962,$(realpath reads/SRR24826962.fastq.gz)" | tee -a samplesheet.csv
          echo "ntc-bc15,$(realpath reads/ntc-bc15.fastq.gz)" | tee -a samplesheet.csv
          echo "ntc-bc31,$(realpath reads/ntc-bc31.fastq.gz)" | tee -a samplesheet.csv
          echo "ntc-bc47,$(realpath reads/ntc-bc47.fastq.gz)" | tee -a samplesheet.csv
      - name: Cache subsampled influenza.fna
        uses: actions/cache@v4
        id: cache-influenza-fna
        with:
          path: influenza-10k.fna.zst
          key: influenza-fna
      - name: Subsample NCBI influenza.fna
        if: steps.cache-influenza-fna.outputs.cache-hit != 'true'
        run: |
          curl --silent -SLk ${FASTA_ZST_URL} | zstdcat | seqtk sample -s 789 - 10000 | zstd -ck > influenza-10k.fna.zst
      - name: Cache influenza.csv
        uses: actions/cache@v4
        id: cache-influenza-csv
        with:
          path: influenza.csv.zst
          key: influenza-csv
      - name: Download influenza.csv
        if: steps.cache-influenza-csv.outputs.cache-hit != 'true'
        run: |
          curl --silent -SLk ${CSV_ZST_URL} > influenza.csv.zst
      - name: Run pipeline with test data
        run: |
          nextflow run ${GITHUB_WORKSPACE} \
            -profile test_nanopore,docker \
            --platform nanopore \
            --input samplesheet.csv \
            --ncbi_influenza_fasta influenza-10k.fna.zst \
            --ncbi_influenza_metadata influenza.csv.zst
      - name: Tree of results
        run: tree -h results/
      - name: Upload .nextflow.log
        uses: actions/upload-artifact@v4
        with:
          name: nextflow-log-nanopore-${{ matrix.nxf_ver }}
          path: .nextflow.log
      - name: Upload pipeline_info/
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: nanopore-test-results-pipline_info-${{ matrix.nxf_ver }}
          path: results/pipeline_info
      - name: Upload nf-flu-subtyping-report.xlsx
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: nanopore-test-results-subtyping-report-${{ matrix.nxf_ver }}
          path: results/nf-flu-subtyping-report.xlsx
      - name: Upload multiqc_report.html
        if: success()
        uses: actions/upload-artifact@v4
        with:
          name: nanopore-test-results-multiqc-${{ matrix.nxf_ver }}
          path: results/MultiQC/multiqc_report.html