Merge pull request #1346 from khersameesh24/spatialxe

#1345 - Testdata for the spatialxe pipeline
nf-core · Oct 14, 2024 · 2a51e41 · 2a51e41
2 parents 5815d2c + 5709f68
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diff --git a/testdata/.end-of-run b/testdata/.end-of-run
diff --git a/testdata/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip b/testdata/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip
diff --git a/testdata/analysis.tar.gz b/testdata/analysis.tar.gz
diff --git a/testdata/analysis.zarr.zip b/testdata/analysis.zarr.zip
diff --git a/testdata/analysis_summary.html b/testdata/analysis_summary.html
diff --git a/testdata/aux_outputs.tar.gz b/testdata/aux_outputs.tar.gz
diff --git a/testdata/cell_boundaries.csv.gz b/testdata/cell_boundaries.csv.gz
diff --git a/testdata/cell_boundaries.parquet b/testdata/cell_boundaries.parquet
diff --git a/testdata/cell_feature_matrix.h5 b/testdata/cell_feature_matrix.h5
diff --git a/testdata/cell_feature_matrix.tar.gz b/testdata/cell_feature_matrix.tar.gz
diff --git a/testdata/cell_feature_matrix.zarr.zip b/testdata/cell_feature_matrix.zarr.zip
diff --git a/testdata/cells.csv.gz b/testdata/cells.csv.gz
diff --git a/testdata/cells.parquet b/testdata/cells.parquet
diff --git a/testdata/cells.zarr.zip b/testdata/cells.zarr.zip
diff --git a/testdata/experiment.xenium b/testdata/experiment.xenium
@@ -0,0 +1,56 @@
+{
+    "major_version": 5,
+    "minor_version": 0,
+    "patch_version": 0,
+    "run_name": "run",
+    "run_start_time": "2024-05-29T00:14:01Z",
+    "region_name": "region",
+    "preservation_method": "fresh_frozen",
+    "num_cells": 36,
+    "transcripts_per_cell": 18,
+    "transcripts_per_100um": 19.666651647839945,
+    "region_area": 3958.2614062499997,
+    "total_cell_area": 2359.3238356411457,
+    "thickness_of_high_quality_decoded_transcripts": 9.126507181720186,
+    "nuclear_transcripts_per_100um": 28.29280705028081,
+    "fraction_transcripts_assigned": 0.8738229755178908,
+    "segmented_cell_stain_frac": 0.9166666666666666,
+    "segmented_cell_boundary_frac": 0.4166666666666667,
+    "segmented_cell_interior_frac": 0.5,
+    "segmented_cell_nuc_expansion_frac": 0.08333333333333333,
+    "imported_cell_frac": 0.0,
+    "cassette_name": "cassette",
+    "slide_id": "slide",
+    "panel_type": "predesigned",
+    "panel_design_id": "mAtlas_v1",
+    "panel_predesigned_id": "",
+    "panel_name": "Xenium Mouse 5K Pan Tissue & Pathways Panel",
+    "panel_organism": "Mouse",
+    "panel_tissue_type": "Multi",
+    "panel_num_targets_predesigned": 5006,
+    "panel_num_targets_custom": 0,
+    "chemistry_version": "v2",
+    "pixel_size": 0.2125,
+    "instrument_sn": "R&D",
+    "instrument_sw_version": "R&D",
+    "analysis_sw_version": "xenium-3.0.0.15",
+    "analysis_uuid": "555b2f80-53d3-421f-80c3-77197a148685",
+    "experiment_uuid": "4f477cff-ec43-4e64-a723-b0017e7494c9",
+    "cassette_uuid": "d14dede1-b15e-42e9-84b7-f98798afaf24",
+    "roi_uuid": "d4c2d423-83ed-4e44-8dfd-a0072bcc3afc",
+    "z_step_size": 3.0,
+    "well_uuid": "def_a31d7c1d_rec_24e100ee",
+    "calibration_uuid": "b6842711-475f-473d-9b2c-13cf2a034535",
+    "images": {
+        "morphology_filepath": "morphology.ome.tif",
+        "morphology_focus_filepath": "morphology_focus/morphology_focus_0000.ome.tif"
+    },
+    "xenium_explorer_files": {
+        "transcripts_zarr_filepath": "transcripts.zarr.zip",
+        "cells_zarr_filepath": "cells.zarr.zip",
+        "cell_features_zarr_filepath": "cell_feature_matrix.zarr.zip",
+        "analysis_zarr_filepath": "analysis.zarr.zip",
+        "analysis_summary_filepath": "analysis_summary.html"
+    },
+    "segmentation_stain": "Xenium Multi-Tissue Stain"
+}