ASCC multi-assembly re-write #369
Workflow file for this run
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| 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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/ascc') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Download test data | |
| # Download A fungal test data set that is full enough to show some real output. | |
| run: | | |
| curl https://tolit.cog.sanger.ac.uk/test-data/resources/ascc/asccTinyTest_V2.tar.gz | tar xzf - | |
| cp /home/runner/work/ascc/ascc/asccTinyTest_V2/assembly/pyoelii_tiny_testfile_with_adapters.fa /home/runner/work/ascc/ascc/asccTinyTest_V2/assembly/Pyoeliiyoelii17XNL_assembly_hap.fa | |
| - name: Temporary ASCC Diamond Data | |
| run: | | |
| curl https://dp24.cog.sanger.ac.uk/ascc/diamond.dmnd -o diamond.dmnd | |
| - name: Temporary BLASTN Data | |
| run: | | |
| curl https://dp24.cog.sanger.ac.uk/blastn.tar.gz | tar xzf - | |
| - name: Temporary Accession2TaxID Data | |
| run: | | |
| curl https://dp24.cog.sanger.ac.uk/ascc/accession2taxid.tar.gz | tar -xzf - | |
| - name: Download the NCBI taxdump database | |
| run: | | |
| mkdir ncbi_taxdump | |
| curl -L https://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz | tar -C ncbi_taxdump -xzf - | |
| - name: Download the FCS-gx database | |
| run: | | |
| mkdir FCS_gx | |
| wget -cq https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.taxa.tsv -O FCS_gx/all.taxa.tsv | |
| wget -cq https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxi -O FCS_gx/all.gxi | |
| wget -cq https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxs -O FCS_gx/all.gxs | |
| wget -cq https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.meta.jsonl -O FCS_gx/all.meta.jsonl | |
| wget -cq https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.blast_div.tsv.gz -O FCS_gx/all.blast_div.tsv.gz | |
| - name: Download the BUSCO lineage database | |
| run: | | |
| mkdir busco_database | |
| curl -L https://tolit.cog.sanger.ac.uk/test-data/resources/busco/blobtoolkit.GCA_922984935.2.2023-08-03.lineages.tar.gz | tar -C busco_database -xzf - | |
| - name: Download the kraken2 database | |
| run: | | |
| mkdir kraken2 | |
| curl -L https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/kraken2.tar.gz | tar -C kraken2 -xzf - | |
| - name: Download the subset of NT database | |
| run: | | |
| mkdir NT_database | |
| curl -L https://ftp.ncbi.nlm.nih.gov/blast/db/18S_fungal_sequences.tar.gz | tar -C NT_database -xzf - | |
| - name: Download the subset of Diamond database | |
| run: | | |
| mkdir diamond | |
| wget -c https://tolit.cog.sanger.ac.uk/test-data/resources/diamond/UP000000212_1234679_tax.dmnd -O diamond/UP000000212_1234679_tax.dmnd | |
| - name: Download the vecscreen test data | |
| run: | | |
| mkdir vecscreen | |
| curl -L https://ftp.ncbi.nlm.nih.gov/blast/db/v4/16SMicrobial_v4.tar.gz | tar -C vecscreen -xzf - | |
| - name: Run FULL pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} \ | |
| -profile test,docker \ | |
| -params-file ${GITHUB_WORKSPACE}/assets/github_testing/github_test.yaml \ | |
| --input ${GITHUB_WORKSPACE}/assets/github_testing/samplesheet.csv \ | |
| --exclude btk_busco \ | |
| --organellar_exclude btk_busco | |
| - name: Upload Nextflow log | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nextflow-${{ strategy.job-index }}-log | |
| path: /home/runner/work/ascc/ascc/.nextflow.log | |
| if-no-files-found: warn | |
| include-hidden-files: true | |
| retention-days: 1 | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| pattern: nextflow-* | |
| merge-multiple: true |