add vecscreen test set on ci, checkin coverage related scripts, updat… #78
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 | |
| 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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/ascc') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ 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.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 -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.taxa.tsv -O FCS_gx/all.taxa.tsv | |
| wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxi -O FCS_gx/all.gxi | |
| wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.gxs -O FCS_gx/all.gxs | |
| wget -c https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.meta.jsonl -O FCS_gx/all.meta.jsonl | |
| wget -c 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 | |
| wget -c https://tolit.cog.sanger.ac.uk/test-data/resources/vecscreen/GCA_900155405.1_PRJEB18760_genomic.fna -O vecscreen/GCA_900155405.1_PRJEB18760_genomic.fna | |
| - name: Run 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 ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results |