Prepare for v0.3.0 #36
Workflow file for this run
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| name: MetaQuest Automation | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| run_metaquest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v2 | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install Dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Install metaquest | |
| run: | | |
| pip install . | |
| - name: Download and setup Mastiff | |
| run: | | |
| curl -o mastiff -L https://github.com/sourmash-bio/mastiff/releases/latest/download/mastiff-client-x86_64-unknown-linux-musl | |
| chmod +x mastiff | |
| mkdir -p $HOME/.local/bin | |
| cp mastiff $HOME/.local/bin/mastiff | |
| echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| mastiff --version | |
| - name: Download Fasta from NCBI | |
| run: | | |
| metaquest download_test_genome | |
| - name: Run Mastiff | |
| run: | | |
| metaquest mastiff --genomes-folder genomes --matches-folder matches | |
| - name: parse_containment | |
| run: metaquest parse_containment --matches_folder matches --parsed_containment_file parsed_containment.txt --summary_containment_file summary_containment.txt | |
| - name: Plot containment | |
| run: metaquest plot_containment --file_path parsed_containment.txt --colors black --save_format png --threshold 0.05 --plot_type rank | |
| - name: Download Metadata | |
| run: metaquest download_metadata --email [email protected] --matches_folder matches --metadata_folder metadata --threshold 0.95 | |
| - name: Parse Metadata | |
| run: metaquest parse_metadata --metadata-folder metadata --metadata-table-file parsed_metadata.txt | |
| - name: Calculate metadata Count | |
| run: metaquest genome_count --summary-file parsed_containment.txt --metadata-file parsed_metadata.txt --metadata-column Sample_Scientific_Name --threshold 0.95 --output-file counts_Sample_Scientific_Name.txt | |
| - name: Plot metadata counts | |
| run: metaquest plot_metadata_counts --file_path counts_Sample_Scientific_Name.txt --plot_type bar --save_format png --colors black | |
| - name: Single Sample | |
| run: metaquest single_sample --summary-file parsed_containment.txt --metadata-file parsed_metadata.txt --summary-column GCF_000008985.1 --metadata-column Sample_Scientific_Name --threshold 0.95 |