Add entries for pangolin-data/-assignment, update workflows #693
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| name: pangolin-ubuntu | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| run_pangolin_test: | |
| name: Pangolin test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: environment.yml | |
| activate-environment: pangolin | |
| channels: conda-forge,bioconda,defaults | |
| - name: Install pangolin | |
| run: pip install -e . | |
| - name: Check pangolin version | |
| run: pangolin --version | |
| - name: Run pangolin with test data | |
| run: pangolin pangolin/test/test_seqs.fasta 2>&1 | tee pangolin.log | |
| - name: Compare assigned lineages (first two columns only) with expected values | |
| run: cut -d, -f1,2 lineage_report.csv | diff - pangolin/test/test_seqs.assignments.csv | |
| - name: Run pangolin with test zip data | |
| run: pangolin pangolin/test/test_seqs.fasta.gz 2>&1 | tee pangolin_zip.log | |
| - name: Run pangolin with test all cache data | |
| run: pangolin pangolin/test/all_bad_seqs.fasta 2>&1 | tee pangolin_all_bad.log | |
| - name: Run pangolin with test all bad data | |
| run: pangolin pangolin/test/all_hash.fasta 2>&1 | tee pangolin_cache.log | |
| - name: Run pangolin usher with test data | |
| run: pangolin --analysis-mode usher pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_usher.log | |
| - name: Run pangolin accurate with test data | |
| run: pangolin --analysis-mode accurate pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_accurate.log | |
| - name: Run pangolin with outdir and outfile | |
| run: pangolin pangolin/test/test_seqs.fasta -o my_test --outfile pangolin_out.txt 2>&1 | tee pangolin_outdir_outfile.log | |
| - name: Run pangolin with out alignment | |
| run: pangolin pangolin/test/test_seqs.fasta --alignment --alignment-file my_alignment.fasta 2>&1 | tee pangolin_alignment.log | |
| - name: Run pangolin aliases | |
| run: pangolin --aliases 2>&1 | tee pangolin_alias.log | |
| - name: Run pangolin all versions | |
| run: pangolin --all-versions 2>&1 | tee pangolin_versions.log | |
| - name: Run pangolin skip designation cache | |
| run: pangolin pangolin/test/test_seqs.fasta --skip-designation-cache 2>&1 | tee pangolin_no_cache.log | |
| - name: Run pangolin update | |
| run: pangolin --update 2>&1 | tee pangolin_update.log | |
| - name: Run pangolin update data | |
| run: pangolin --update-data 2>&1 | tee pangolin_update_data.log | |
| - name: Run pangolin verbose mode | |
| run: pangolin --verbose pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_verbose.log | |
| - name: Add assignment cache | |
| run: pangolin --add-assignment-cache | |
| - name: remove assignment cache | |
| run: pip uninstall -y pangolin-assignment |