upd readme - citation #88
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| name: Open Tree of Life tests | |
| # This workflow runs tests for the OToL-related part of the PhyloNext pipeline | |
| on: push | |
| jobs: | |
| biodiverse-tests: | |
| name: Run OToL tests | |
| runs-on: ubuntu-latest | |
| container: | |
| image: vmikk/opentree:1.4.0 | |
| volumes: | |
| - ${{ github.workspace }}:/ott | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: main | |
| fetch-depth: 1 | |
| # pwd = /__w/PhyloNext/PhyloNext | |
| - name: Fetching test tree from OToL | |
| run: | | |
| python \ | |
| /__w/PhyloNext/PhyloNext/bin/induced_synth_subtree_from_csv.py \ | |
| --query /__w/PhyloNext/PhyloNext/test_data/Felidae,Canidae_Species_OTT.csv \ | |
| --output_dir $(pwd)/OTT/ \ | |
| --phylo-only \ | |
| --max-age 111 | |
| - name: Verifying results | |
| run: | | |
| ls -l $(pwd)/OTT/ | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v2 | |
| with: | |
| files: "./OTT/ott_label_dated_tree.tre" | |
| # `file-existence-action` does not intrpret $(pwd)? -> use relative path | |
| - name: Files exist? | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| echo "Looks good, Labeled and dated phylogenetic tree is in place!" | |
| exit 0 | |
| - name: Files are missing? | |
| if: steps.check_files.outputs.files_exists == 'false' | |
| run: | | |
| echo "ERROR! Some files are missing!" | |
| exit 1 |