Murchie2023 #2999
Workflow file for this run
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: check_dataset | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| on: | |
| pull_request: | |
| branches: [master] | |
| jobs: | |
| AMDirT: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| architecture: "x64" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install amdirt==1.5.0 | |
| pip install jsonschema==4.17.0 | |
| - name: Make validation results directory | |
| run: mkdir validation/ | |
| - name: Add AMDirT validate version | |
| run: | | |
| echo "$(AMDirT --version)" > validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient host-associated metagenome (e.g. microbiomes) | |
| if: always() | |
| run: | | |
| echo "# Samples" >> validation/validation_results_raw.txt | |
| echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient single microbial genomes (e.g. pathogens) | |
| if: always() | |
| run: | | |
| echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: SAMPLES test ancient environmental (e.g. sediment) | |
| if: always() | |
| run: | | |
| echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient host-associated metagenome (e.g. microbiomes) | |
| if: always() | |
| run: | | |
| echo "# Libraries" >> validation/validation_results_raw.txt | |
| echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient host-associated single-genomes (e.g. pathogens) | |
| if: always() | |
| run: | | |
| echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: LIBRARIES test ancient environmental metagenomes (e.g. sedaDNA) | |
| if: always() | |
| run: | | |
| echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
| AMDirT validate -s -d -c -m ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json &>> validation/validation_results_raw.txt | |
| - name: cleanup validation results from streamlit warnings | |
| if: always() | |
| run: | | |
| grep -v streamlit validation/validation_results_raw.txt > validation/validation_results.txt | |
| - uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: results | |
| path: validation/validation_results.txt | |
| - uses: actions/download-artifact@v3 | |
| if: always() | |
| with: | |
| name: results | |
| - name: comment PR | |
| if: always() | |
| uses: mshick/add-pr-comment@v2 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| message-path: validation/validation_results.txt | |
| refresh-message-position: true |