fix EDGE2 reference #67
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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:1.3.0 | |
| 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 |