Added pipeline ingestion YAML documentation #34
Workflow file for this run
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| name: Tutorials CI | |
| 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: ["3.9"] | |
| steps: | |
| # - uses: actions/checkout@v4 | |
| - name: Download Conda YAML file | |
| run: curl -o pipeline_env.yaml https://raw.githubusercontent.com/DendrouLab/panpipes/kra-gha/pipeline_env.yaml | |
| - 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 # consider moving to etc/pipeline_env.yaml | |
| - 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 | |
| #- name: Run tests | |
| # shell: bash -el {0} | |
| # run: | | |
| # python -m pytest tests/ | |
| # 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: Replace template contents in configuration file | |
| run: | | |
| cd teaseq/ingest | |
| sed -i 's+panpipes-tutorials/tutorials/ingesting_data/qc_genelist_1.0.csv+qc_genelist_1.0.csv+g' pipeline.yml | |
| - name: File tree | |
| if: env.debug == 'true' | |
| run: tree | |
| - 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 |