Prepare test data #9
Workflow file for this run
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| name: Prepare test data | |
| on: | |
| workflow_dispatch: | |
| # uncomment and adjust the branch name if you need to add new datasets to the artifact | |
| # push: | |
| # branches: | |
| # - main | |
| jobs: | |
| prepare-data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download test datasets | |
| run: | | |
| mkdir -p ./data | |
| cd ./data | |
| # 10x Genomics Xenium 2.0.0 | |
| curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip | |
| curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip | |
| # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation | |
| # this file seems to be corrupted; skipping it for now | |
| # curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip | |
| # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion | |
| curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip | |
| # Spatial Genomics seqFISH v2 | |
| curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip | |
| - name: Unzip files | |
| run: | | |
| cd ./data | |
| for file in *.zip; do | |
| dir="${file%.zip}" | |
| mkdir -p "$dir" | |
| unzip "$file" -d "$dir" | |
| rm "$file" | |
| done | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: data | |
| path: ./data |