update scripts

openproblems-bio · Jan 30, 2025 · 6dc6678 · 6dc6678
1 parent ae69889
commit 6dc6678
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Showing 2 changed files with 1 addition and 2 deletions.
diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh
@@ -36,7 +36,7 @@ mkdir -p $DATASET_DIR
 python << HERE
 import anndata as ad
 
-adata = ad.read_h5ad("resources_test/task_cyto_batch_integration/starter_file/original_dataset.h5ad")
+adata = ad.read_h5ad("resources_test/task_cyto_batch_integration/starter_file/common_dataset.h5ad")
 
 channelsofinterest = ['UV379-A',
  'UV515-A',

diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh
@@ -24,6 +24,5 @@ nextflow run . \
   --input_unintegrated_censored resources_test/task_cyto_batch_integration/starter_file/unintegrated_censored.h5ad \
   --input_unintegrated resources_test/task_cyto_batch_integration/starter_file/unintegrated.h5ad \
   --input_validation resources_test/task_cyto_batch_integration/starter_file/validation.h5ad \
-  --samples_to_compare "Tube1_Batch1_WT;Tube1_Batch2_WT" \
   --output_state state.yaml \
   --publish_dir "$publish_dir"