adding pan_clade option to squirrel alignment #441
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| name: squirrel | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| run_squirrel_test: | |
| name: squirrel test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["ubuntu-latest","macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: false | |
| environment-file: environment.yml | |
| activate-environment: squirrel | |
| channels: conda-forge,bioconda,defaults | |
| miniforge-version: latest | |
| - name: Install squirrel | |
| run: pip install -e . | |
| - name: Check squirrel version | |
| run: squirrel --version | |
| - name: Run squirrel with test data | |
| run: squirrel squirrel/data/NC_063383.fasta 2>&1 | tee squirrel.log | |
| - name: Run squirrel phylo with test data | |
| run: squirrel ./test/cI_test.with_og.fasta --clade cladei --run-phylo --outgroups 'JX878419' 2>&1 | tee squirrel_phylo.log | |
| - name: Run squirrel seq qc with test data | |
| run: squirrel ./test/cI_test.with_og.fasta --clade cladei --run-phylo --outgroups 'JX878419' --seq-qc --assembly-refs squirrel/data/ref_seq.fasta 2>&1 | tee squirrel_qc.log | |
| - name: Run squirrel --include-background with test data | |
| run: squirrel ./test/cI_test.fasta --clade cladei --run-phylo --include-background 2>&1 | tee squirrel_bg.log | |
| - name: Run squirrel --include-background with test data and outdir specified and seqqc | |
| run: squirrel ./test/cI_test.fasta --clade cladei -o squirrel_output --run-phylo --seq-qc --include-background 2>&1 | tee squirrel_bg.log | |
| - name: Run squirrel --include-background with test data and outdir specified and seqqc with clade split | |
| run: squirrel ./test/varied_test.fasta --clade split -o squirrel_output --run-phylo --seq-qc --include-background 2>&1 | tee squirrel_split.log | |
| - name: Run squirrel variola | |
| run: squirrel ./test/cI_test.fasta --clade variola -o squirrel_output --run-phylo --seq-qc --include-background 2>&1 | tee squirrel_var.log | |
| - name: Run squirrel clade i and og and background | |
| run: squirrel ./test/cI_test.fasta --clade cladei -o squirrel_double_og_test --outgroups 'KJ642615|human|Nigeria||1978' -a --seq-qc --include-background 2>&1 | tee squirrel_var.log |