From MuData to SpatialData #543
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: Run tutorials (ingestion) | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| env: | |
| debug: 'true' | |
| jobs: | |
| ingestion: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] # , "macos-latest", "windows-latest" | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| auto-activate-base: true | |
| auto-update-conda: true | |
| channels: conda-forge | |
| channel-priority: strict | |
| activate-environment: pipeline_env | |
| environment-file: pipeline_env.yaml | |
| - name: Install Panpipes | |
| shell: bash -el {0} | |
| run: | | |
| pip install -e . | |
| conda list | |
| - name: Conda info | |
| if: env.debug == 'true' | |
| shell: bash -el {0} | |
| run: conda info | |
| - name: Conda list | |
| if: env.debug == 'true' | |
| shell: pwsh | |
| run: conda list | |
| # Note: all three files are renamed during the download to trim the "subsample_" prefix | |
| - name: Preparing the data | |
| run: | | |
| mkdir -p teaseq/ingest/data.dir | |
| cd teaseq/ingest/data.dir | |
| curl -L -o adt.h5ad https://figshare.com/ndownloader/files/41671551 | |
| curl -L -o atac.h5ad https://figshare.com/ndownloader/files/41671554 | |
| curl -L -o rna.h5ad https://figshare.com/ndownloader/files/41671557 | |
| # Note: we run the following to test that the commands works | |
| # However, the following task will replacing the file anyway | |
| - name: Preparing the configuration file | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/ingest | |
| panpipes ingest config | |
| - name: Edit the submission file | |
| run: | | |
| cd teaseq/ingest | |
| curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/9a4fcbc3c0a4fdc8e6578d086a88730f/pipeline.yml | |
| - name: Preparing the submission file | |
| run: | | |
| cd teaseq/ingest | |
| curl -o sample_file_qc.txt https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/40ed291bf9a7ff73c4f396ec63cff2f7/sample_file_qc.txt | |
| - name: Preparing the QC gene lists | |
| run: | | |
| cd teaseq/ingest | |
| curl -o qc_genelist_1.0.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/fd38f25644105ea357a26e78a59139bb/qc_genelist_1.0.csv | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree teaseq | |
| - name: Review pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/ingest | |
| panpipes ingest show full --local | |
| - name: Run pipeline tasks | |
| shell: bash -el {0} | |
| run: | | |
| cd teaseq/ingest | |
| panpipes ingest make full --local | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree teaseq | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: teaseq_unfilt.h5mu | |
| path: teaseq/ingest/teaseq_unfilt.h5mu | |
| retention-days: 1 |