Many additions #237
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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: | |
| - "22.10.1" | |
| - "latest-everything" | |
| steps: | |
| - name: Get branch names | |
| # Pulls the names of current branches in repo | |
| # steps.branch-names.outputs.current_branch is used later and returns the name of the branch the PR is made FROM not to | |
| id: branch-names | |
| uses: tj-actions/branch-names@v8 | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Singularity | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Setup apptainer | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install nf-core | |
| run: | | |
| pip install nf-core | |
| - name: NF-Core Download - download singularity containers | |
| # Forcibly download repo on active branch and download SINGULARITY containers into the CACHE dir if not found | |
| # Must occur after singularity install or will crash trying to dl containers | |
| # Zip up this fresh download and run the checked out version | |
| run: | | |
| nf-core download sanger-tol/ascc --revision ${{ steps.branch-names.outputs.current_branch }} --compress none -d --force --outdir sanger-ascc --container-cache-utilisation amend --container-system singularity | |
| - 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 - | |
| - 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 pacbio barcode | |
| run: | | |
| mkdir pacbio_barcode | |
| wget -O pacbio_barcode/SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.fasta_.zip -c https://www.pacb.com/wp-content/uploads/SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.fasta_.zip | |
| cd pacbio_barcode | |
| unzip SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.fasta_.zip | |
| mv SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.fasta pacbio_adaptors.fa | |
| rm -rf SMRTbell_Barcoded_Adapter_Plate_3.0_bc2001-bc2096.fasta_.zip __MACOSX | |
| cd ../ | |
| - 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 - | |
| ls -lh | |
| - name: Singularity - Run FULL pipeline with test data | |
| # 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 ./sanger-ascc/${{ steps.branch-names.outputs.current_branch }}/main.nf -profile test,singularity --outdir ./results --include ALL --exclude btk_busco |