schema upd - add nexus trees #80
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| name: Biodiverse tests | |
| # This workflow runs tests for the Biodiverse-relate part of the PhyloNext pipeline | |
| on: push | |
| jobs: | |
| biodiverse-tests: | |
| name: Run Biodiverse tests | |
| runs-on: ubuntu-latest | |
| container: | |
| image: vmikk/biodiverse:1.4.0 | |
| volumes: | |
| - ${{ github.workspace }}:/biodiverse | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: main | |
| fetch-depth: 1 | |
| # pwd = /__w/PhyloNext/PhyloNext | |
| - name: Preparing Biodiverse input file | |
| run: | | |
| mkdir -p Biodiverse_Test | |
| perl /__w/PhyloNext/PhyloNext/bin/00_create_bds.pl \ | |
| --csv_file /__w/PhyloNext/PhyloNext/test_data/Biodiverse_tests/FelidaeCanidae_occurrences.csv \ | |
| --out_file $(pwd)/Biodiverse_Test/occ.bds \ | |
| --label_column_number '0' \ | |
| --group_column_number_x '1'\ | |
| --cell_size_x '-1' | |
| - name: Preparing the tree for Biodiverse | |
| run: | | |
| perl /__w/PhyloNext/PhyloNext/bin/00_create_bts.pl \ | |
| --input_tree_file /__w/PhyloNext/PhyloNext/test_data/Biodiverse_tests/FelidaeCanidae_tree.nex \ | |
| --out_file $(pwd)/Biodiverse_Test/tree.bts | |
| - name: Running biodiversity analyses | |
| run: | | |
| perl /__w/PhyloNext/PhyloNext/bin/02_biodiverse_analyses.pl \ | |
| --input_bds_file $(pwd)/Biodiverse_Test/occ.bds \ | |
| --input_bts_file $(pwd)/Biodiverse_Test/tree.bts \ | |
| --calcs calc_richness,calc_pd,calc_pe | |
| - name: Testing data export | |
| run: | | |
| perl /__w/PhyloNext/PhyloNext/bin/04_load_bds_and_export_results.pl \ | |
| --input_bds_file $(pwd)/Biodiverse_Test/occ_analysed.bds \ | |
| --output_csv_prefix $(pwd)/Biodiverse_Test/RND | |
| - name: Verifying results | |
| run: | | |
| echo -e "Output file list:\n" | |
| ls -l $(pwd)/Biodiverse_Test | |
| echo -e "\nHead of RND_SPATIAL_RESULTS.csv:\n" | |
| head -5 $(pwd)/Biodiverse_Test/RND_SPATIAL_RESULTS.csv | |
| - name: Check file existence | |
| id: check_files | |
| uses: andstor/file-existence-action@v2 | |
| with: | |
| files: "./Biodiverse_Test/RND_SPATIAL_RESULTS.csv, ./Biodiverse_Test/occ_analysed.bds, ./Biodiverse_Test/occ.bds, ./Biodiverse_Test/tree.bts" | |
| - name: File exists | |
| if: steps.check_files.outputs.files_exists == 'true' | |
| run: | | |
| echo "Looks good, all expected output files are in place!" | |
| exit 0 | |
| - name: File is missing | |
| if: steps.check_files.outputs.files_exists == 'false' | |
| run: | | |
| echo "ERROR! Some files are missing!" | |
| exit 1 |