diff --git a/modules/nf-neuro/preproc/eddy/main.nf b/modules/nf-neuro/preproc/eddy/main.nf
index dd1c5ef5..a50fef51 100644
--- a/modules/nf-neuro/preproc/eddy/main.nf
+++ b/modules/nf-neuro/preproc/eddy/main.nf
@@ -114,32 +114,36 @@ process PREPROC_EDDY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    scil_volume_math.py -h
-    maskfilter -h
-    bet -h
-    scil_dwi_extract_b0.py -h
-    scil_gradients_validate_correct_eddy.py -h
-    scil_dwi_concatenate.py -h
-    mrconvert -h
-    scil_dwi_prepare_eddy_command.py -h
-    scil_header_print_info.py -h
-
     touch ${prefix}__dwi_corrected.nii.gz
     touch ${prefix}__dwi_eddy_corrected.bval
     touch ${prefix}__dwi_eddy_corrected.bvec
     touch ${prefix}__b0_bet_mask.nii.gz
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
-
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    scil_volume_math.py -h
+    maskfilter -h
+    bet -h
+    scil_dwi_extract_b0.py -h
+    scil_gradients_validate_correct_eddy.py -h
+    scil_dwi_concatenate.py -h
+    mrconvert -h
+    scil_dwi_prepare_eddy_command.py -h
+    scil_header_print_info.py -h
     """
 }
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
index bfe7eb1b..bc5d31ab 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
@@ -93,4 +93,34 @@ nextflow_process {
             )
         }
     }
+
+    test("eddy - stub-run") {
+        options "-stub-run"
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ], // meta map
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01__corrected_b0s.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_fieldcoef.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_movpar.txt", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
index 239baba4..617a4012 100644
--- a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
+++ b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
@@ -62,5 +62,17 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-11-21T19:53:14.315721034"
+    },
+    "eddy - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,137e3ce0fd25e5b16de2d8cc5a5aefca"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T12:50:30.654366"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/preproc/topup/main.nf b/modules/nf-neuro/preproc/topup/main.nf
index 99fa3412..3299c91b 100644
--- a/modules/nf-neuro/preproc/topup/main.nf
+++ b/modules/nf-neuro/preproc/topup/main.nf
@@ -73,16 +73,10 @@ process PREPROC_TOPUP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def prefix_topup = task.ext.prefix_topup ? task.ext.prefix_topup : ""
 
     """
-    scil_volume_math.py -h
-    scil_dwi_extract_b0.py -h
-    antsRegistrationSyNQuick.sh -h
-    scil_dwi_prepare_topup_command.py -h
-
     touch ${prefix}__corrected_b0s.nii.gz
     touch ${prefix}__rev_b0_warped.nii.gz
     touch ${prefix}__rev_b0_mean.nii.gz
@@ -95,7 +89,18 @@ process PREPROC_TOPUP {
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         antsRegistration: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
-
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    scil_volume_math.py -h
+    scil_dwi_extract_b0.py -h
+    antsRegistrationSyNQuick.sh
+    scil_dwi_prepare_topup_command.py -h
     """
 }
diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test b/modules/nf-neuro/preproc/topup/tests/main.nf.test
index f404355c..146ceb93 100644
--- a/modules/nf-neuro/preproc/topup/tests/main.nf.test
+++ b/modules/nf-neuro/preproc/topup/tests/main.nf.test
@@ -95,4 +95,32 @@ nextflow_process {
             )
         }
     }
+
+    test("topup - stub-run") {
+        options "-stub-run"
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ], // meta map
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_sbref.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_sbref.nii.gz", checkIfExists: true)]}
+                input[1] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap b/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
index efe20842..171632b7 100644
--- a/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
+++ b/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
@@ -33,6 +33,18 @@
         },
         "timestamp": "2024-11-01T16:21:18.752887499"
     },
+    "topup - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,1e46217f093e27a6a26cd479f074296b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T11:56:01.860981"
+    },
     "topup_light": {
         "content": [
             "test__corrected_b0s.nii.gz",