Prepare test data #25
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| name: Prepare test data | |
| on: | |
| schedule: | |
| - cron: "0 0 1 * *" # run once a month to prevent artifact expiration | |
| 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@v4 | |
| - name: Download test datasets | |
| run: | | |
| mkdir -p ./data | |
| cd ./data | |
| # ------- | |
| # the Xenium datasets are licensed as CC BY 4.0, as shown here | |
| # https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/resources/xenium-example-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 | |
| # 10x Genomics Xenium 4.0.0 (v1) Human ovary, nuclear expansion | |
| curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip | |
| # 10x Genomics Xenium 4.0.0 (v1) Human ovary, multimodal cell segmentation | |
| curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip | |
| # 10x Genomics Xenium 4.0.0 (v1+Protein) Human kidney, multimodal cell segmentation | |
| curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip | |
| # ------- | |
| # the Visium HD dataset is licensed as CC BY 4.0, as shown here | |
| # https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data | |
| # 10x Genomics Visium HD 4.0.1 3' Mouse Brain | |
| curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip | |
| # ------- | |
| # we received written permission to make the following dataset public and integrate it in the CI system of spatialdata-io | |
| # 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@v4 | |
| with: | |
| name: data | |
| path: ./data |