Update NCBI metadata #316
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| name: Update NCBI metadata | |
| on: | |
| schedule: | |
| - cron: '0 0 */7 * *' | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.repository }} | |
| env: | |
| NXF_VER: "24.10.4" | |
| NXF_WORK: ${{ github.workspace }}/work | |
| NXF_OUTPUT: ${{ github.workspace }}/outputs | |
| NXF_NAME: github-${{ github.run_number }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| defaults: | |
| run: | |
| shell: bash -eli {0} | |
| jobs: | |
| fetch_ncbi_metadata: | |
| runs-on: self-hosted | |
| steps: | |
| - name: Checkout main | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Cache envs | |
| id: cache-envs | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ env.NXF_WORK }}/conda | |
| $CONDA_PREFIX/envs | |
| key: env-${{ env.NXF_VER }}-${{ github.job }} | |
| restore-keys: | | |
| env-${{ env.NXF_VER }}-${{ github.job }} | |
| env-${{ env.NXF_VER }} | |
| env- | |
| - name: 'Check and setup conda environment' | |
| run: | | |
| mamba env update --name freyja-sra --file environment.yml --prune | |
| - name: Fetch NCBI metadata | |
| run: | | |
| mamba activate freyja-sra | |
| python scripts/fetch_sra_metadata.py | |
| - name: 'Get updated barcodes and lineages from Freyja repo' | |
| run: | | |
| git clone http://github.com/andersen-lab/Freyja | |
| cp Freyja/freyja/data/usher_barcodes.feather data/ | |
| cp Freyja/freyja/data/lineages.yml data/ | |
| cp Freyja/freyja/data/last_barcode_update.txt data/ | |
| - name: 'Commit and push changes' | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git remote set-url origin https://github.com/andersen-lab/Freyja-SRA | |
| if [[($(git status data/usher_barcodes.feather --porcelain | wc -c) -ne 0)]]; then | |
| git add data/usher_barcodes.feather | |
| git add data/lineages.yml | |
| git add data/last_barcode_update.txt | |
| fi | |
| git add data/all_metadata.csv | |
| git commit -m "Update metadata" | |
| git push --force |