From 6dc667839fec580bf9a9317d84bca8c2d0f0e676 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 30 Jan 2025 11:02:00 +0100
Subject: [PATCH] update scripts

---
 scripts/create_resources/test_resources.sh | 2 +-
 scripts/run_benchmark/run_test_local.sh    | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh
index 191cbe4..ff9b7f4 100755
--- 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
index 275889b..d930a6e 100755
--- 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"