update test resources

openproblems-bio · Aug 28, 2024 · 304d7a9 · 304d7a9
1 parent 998f98b
commit 304d7a9
Showing 1 changed file with 17 additions and 2 deletions.
diff --git a/scripts/generate_test_resource.sh b/scripts/generate_test_resource.sh
@@ -13,14 +13,29 @@ nextflow run . \
   --dataset_summary "MOBNEW" \
   --dataset_reference "..." \
   --dataset_organism "mus_musculus" \
+  --output_state '$id/state.yaml' \
   --publish_dir resources_test/datasets
 
+# run a method
 viash run src/methods/scdesign3/config.vsh.yaml -- \
   --input resources_test/datasets/MOBNEW/dataset_sp.h5ad \
   --output resources_test/datasets/MOBNEW/simulated_dataset.h5ad
 
-viash run src/metrics/ks_statistic/config.vsh.yaml -- \
+# process the simulated spatial dataset
+viash run src/process_datasets/generate_sim_spatialcluster/config.vsh.yaml -- \
+  --input_sp resources_test/datasets/MOBNEW/dataset_sp.h5ad \
+  --input_sp_sim resources_test/datasets/MOBNEW/simulated_dataset.h5ad \
+  --output_sp resources_test/datasets/MOBNEW/simulated_dataset_processed.h5ad
+
+# run a metric
+viash run src/metrics/ks_statistic_spatial/config.vsh.yaml -- \
   --input_spatial_dataset resources_test/datasets/MOBNEW/dataset_sp.h5ad \
   --input_singlecell_dataset resources_test/datasets/MOBNEW/dataset_sc.h5ad \
-  --input_simulated_dataset resources_test/datasets/MOBNEW/simulated_dataset.h5ad \
+  --input_simulated_dataset resources_test/datasets/MOBNEW/simulated_dataset_processed.h5ad \
   --output resources_test/datasets/MOBNEW/score.h5ad
+
+# sync the resources
+aws s3 sync --profile op \
+  resources_test \
+  s3://openproblems-data/resources_test/task_spatial_simulators \
+  --delete --dryrun