Merge pull request #73 from peterk87/add-vadr #131
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |