diff --git a/testing/testing_scripts/test_apply_basic_flatfield_corr.py b/testing/testing_scripts/test_apply_basic_flatfield_corr.py
index 08d8dd4..f22c063 100644
--- a/testing/testing_scripts/test_apply_basic_flatfield_corr.py
+++ b/testing/testing_scripts/test_apply_basic_flatfield_corr.py
@@ -32,7 +32,8 @@ def test_apply_basic_flatfield_corr():
             "work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-flatcorr_SPIM.zarr",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_bids_readme.py b/testing/testing_scripts/test_bids_readme.py
index 5eae1a3..1249950 100644
--- a/testing/testing_scripts/test_bids_readme.py
+++ b/testing/testing_scripts/test_bids_readme.py
@@ -23,6 +23,7 @@ def test_bids_readme():
 
         # dbg
         print("bids/README.md", file=sys.stderr)
+        #Hello
 
         # Run the test job.
         sp.check_output([
@@ -32,12 +33,12 @@ def test_bids_readme():
             "bids/README.md",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
         ])
-
         # Check the output byte by byte using cmp.
         # To modify this behavior, you can inherit from common.OutputChecker in here
         # and overwrite the method `compare_files(generated_file, expected_file), 
diff --git a/testing/testing_scripts/test_bids_samples_json.py b/testing/testing_scripts/test_bids_samples_json.py
index 0ae48a2..f4879b5 100644
--- a/testing/testing_scripts/test_bids_samples_json.py
+++ b/testing/testing_scripts/test_bids_samples_json.py
@@ -32,7 +32,8 @@ def test_bids_samples_json():
             "bids/samples.json",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_blaze_to_metadata.py b/testing/testing_scripts/test_blaze_to_metadata.py
index 8157b04..a17a544 100644
--- a/testing/testing_scripts/test_blaze_to_metadata.py
+++ b/testing/testing_scripts/test_blaze_to_metadata.py
@@ -32,7 +32,8 @@ def test_blaze_to_metadata():
             "bids/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_SPIM.json",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_create_samples_tsv.py b/testing/testing_scripts/test_create_samples_tsv.py
index cac3ae3..4c6824d 100644
--- a/testing/testing_scripts/test_create_samples_tsv.py
+++ b/testing/testing_scripts/test_create_samples_tsv.py
@@ -32,7 +32,8 @@ def test_create_samples_tsv():
             "bids/samples.tsv",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_extract_dataset.py b/testing/testing_scripts/test_extract_dataset.py
index 897a2e9..9f233e8 100644
--- a/testing/testing_scripts/test_extract_dataset.py
+++ b/testing/testing_scripts/test_extract_dataset.py
@@ -32,7 +32,8 @@ def test_extract_dataset():
             "work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-raw_SPIM",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_fit_basic_flatfield_corr.py b/testing/testing_scripts/test_fit_basic_flatfield_corr.py
index 479cd02..845c0b1 100644
--- a/testing/testing_scripts/test_fit_basic_flatfield_corr.py
+++ b/testing/testing_scripts/test_fit_basic_flatfield_corr.py
@@ -32,7 +32,8 @@ def test_fit_basic_flatfield_corr():
             "work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_stain-abeta_basicmodel",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
@@ -42,4 +43,4 @@ def test_fit_basic_flatfield_corr():
         # To modify this behavior, you can inherit from common.OutputChecker in here
         # and overwrite the method `compare_files(generated_file, expected_file), 
         # also see common.py.
-        common.OutputChecker(data_path, expected_path, workdir).check()
+        common.ImperfectOutputChecker(data_path, expected_path, workdir).check()
diff --git a/testing/testing_scripts/test_generate_flatfield_qc.py b/testing/testing_scripts/test_generate_flatfield_qc.py
index 1f84c32..f9e0e7a 100644
--- a/testing/testing_scripts/test_generate_flatfield_qc.py
+++ b/testing/testing_scripts/test_generate_flatfield_qc.py
@@ -36,7 +36,8 @@ def test_generate_flatfield_qc():
             "qc/sub-mouse1_sample-brain_acq-blaze1x/images/uncorr",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_generate_subject_qc.py b/testing/testing_scripts/test_generate_subject_qc.py
index 322a4c1..f589718 100644
--- a/testing/testing_scripts/test_generate_subject_qc.py
+++ b/testing/testing_scripts/test_generate_subject_qc.py
@@ -34,7 +34,8 @@ def test_generate_subject_qc():
             "qc/sub-mouse1_sample-brain_acq-blaze1x/subject.html",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_generate_volume_qc.py b/testing/testing_scripts/test_generate_volume_qc.py
index ebcda56..b2a5510 100644
--- a/testing/testing_scripts/test_generate_volume_qc.py
+++ b/testing/testing_scripts/test_generate_volume_qc.py
@@ -34,7 +34,8 @@ def test_generate_volume_qc():
             "qc/sub-mouse1_sample-brain_acq-blaze1x/volume_qc.html",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_generate_whole_slice_qc.py b/testing/testing_scripts/test_generate_whole_slice_qc.py
index e8d3519..19d3233 100644
--- a/testing/testing_scripts/test_generate_whole_slice_qc.py
+++ b/testing/testing_scripts/test_generate_whole_slice_qc.py
@@ -35,7 +35,8 @@ def test_generate_whole_slice_qc():
             "qc/sub-mouse1_sample-brain_acq-blaze1x/images/whole",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_ome_zarr_to_nii.py b/testing/testing_scripts/test_ome_zarr_to_nii.py
index 11e5304..17df9b9 100644
--- a/testing/testing_scripts/test_ome_zarr_to_nii.py
+++ b/testing/testing_scripts/test_ome_zarr_to_nii.py
@@ -32,7 +32,8 @@ def test_ome_zarr_to_nii():
             "bids/derivatives/resampled/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_stain-abeta_res-3x_SPIM.nii",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_raw_dataset_desc.py b/testing/testing_scripts/test_raw_dataset_desc.py
index 9a38539..2480d87 100644
--- a/testing/testing_scripts/test_raw_dataset_desc.py
+++ b/testing/testing_scripts/test_raw_dataset_desc.py
@@ -32,7 +32,8 @@ def test_raw_dataset_desc():
             "bids/dataset_description.json",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_resampled_dataset_desc.py b/testing/testing_scripts/test_resampled_dataset_desc.py
index b021ad4..47fb87d 100644
--- a/testing/testing_scripts/test_resampled_dataset_desc.py
+++ b/testing/testing_scripts/test_resampled_dataset_desc.py
@@ -32,7 +32,8 @@ def test_resampled_dataset_desc():
             "bids/derivatives/resampled/dataset_description.json",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_tif_to_zarr.py b/testing/testing_scripts/test_tif_to_zarr.py
index 0da0311..6cf9041 100644
--- a/testing/testing_scripts/test_tif_to_zarr.py
+++ b/testing/testing_scripts/test_tif_to_zarr.py
@@ -32,7 +32,8 @@ def test_tif_to_zarr():
             "work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-raw_SPIM.zarr",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
diff --git a/testing/testing_scripts/test_zarr_to_bdv.py b/testing/testing_scripts/test_zarr_to_bdv.py
index f8b6da6..3eed796 100644
--- a/testing/testing_scripts/test_zarr_to_bdv.py
+++ b/testing/testing_scripts/test_zarr_to_bdv.py
@@ -33,7 +33,8 @@ def test_zarr_to_bdv():
             "work/sub-mouse1/micr/sub-mouse1_sample-brain_acq-blaze1x_desc-flatcorr_bdv.xml",
             "-f", 
             "-j1",
-            "--keep-target-files",
+            "--target-files-omit-workdir-adjustment",
+			"--use-singularity",
     
             "--directory",
             workdir,
@@ -43,4 +44,4 @@ def test_zarr_to_bdv():
         # To modify this behavior, you can inherit from common.OutputChecker in here
         # and overwrite the method `compare_files(generated_file, expected_file), 
         # also see common.py.
-        common.OutputChecker(data_path, expected_path, workdir).check()
+        common.ImperfectOutputChecker(data_path, expected_path, workdir).check()