diff --git a/.devcontainer/devops/devcontainer.json b/.devcontainer/devops/devcontainer.json
index ad6788aa..9c044d5a 100755
--- a/.devcontainer/devops/devcontainer.json
+++ b/.devcontainer/devops/devcontainer.json
@@ -4,7 +4,9 @@
         "dockerfile": "Dockerfile",
         "args": {
             "NFTEST_VERSION": "0.9.0",
-            "POETRY_VERSION": "1.8.*"
+            "POETRY_VERSION": "1.8.*",
+            "NFT_DIFF": "pdiff",
+            "NFT_DIFF_ARGS": "--line-numbers --width 120 --expand-tabs=2"
         }
     },
     "forwardPorts": [3000],
diff --git a/.github/workflows/manual_checks.yml b/.github/workflows/manual_checks.yml
new file mode 100644
index 00000000..2b51e6b0
--- /dev/null
+++ b/.github/workflows/manual_checks.yml
@@ -0,0 +1,16 @@
+name: Trigger checks manually
+on:
+  issue_comment:
+    types:
+      - created
+      - edited
+
+jobs:
+  checks:
+    if: github.event.issue.pull_request && contains(github.event.comment.body, '@rerun-checks')
+    # Cancel if a newer run is started
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+      cancel-in-progress: true
+    uses: ./.github/workflows/run_checks_suite.yml
+    secrets: inherit
diff --git a/.github/workflows/update_pr.yml b/.github/workflows/update_pr.yml
index cd600206..4cb09366 100644
--- a/.github/workflows/update_pr.yml
+++ b/.github/workflows/update_pr.yml
@@ -6,7 +6,8 @@ on:
   merge_group:
     types:
       - checks_requested
-    branches: -main
+    branches:
+      - main
 
 # Cancel if a newer run is started
 concurrency:
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 0d7d8836..7270868c 100755
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -19,5 +19,24 @@
     "testDataExplorer.dataserver": "scil.usherbrooke.ca",
     "testDataExplorer.serverdatalocation": "scil_test_data/dvc-store/files/md5",
     "testDataExplorer.localListingLocation": "tests/test_data.json",
-    "testDataExplorer.remoteListingLocation": "tests/test_data.json"
+    "testDataExplorer.remoteListingLocation": "tests/test_data.json",
+    "nextflow.files.exclude": [
+        ".git",
+        ".nf-test",
+        "work",
+        ".venv",
+        ".nextflow",
+        "node_modules",
+        ".tests/runs"
+    ],
+    "cSpell.ignorePaths": [
+        "package-lock.json",
+        "node_modules",
+        "vscode-extension",
+        ".git/",
+        ".vscode",
+        ".vscode-insiders",
+        ".venv",
+        "tests/.runs"
+    ]
 }
diff --git a/cspell.json b/cspell.json
new file mode 100644
index 00000000..c886734e
--- /dev/null
+++ b/cspell.json
@@ -0,0 +1,24 @@
+{
+    "version": "0.2",
+    "dictionaryDefinitions": [
+        {
+            "name": "neuroscience",
+            "path": "docs/cspell/neuroscience.txt",
+            "addWords": true
+        }
+    ],
+    "dictionaries": [
+        "typescript",
+        "node",
+        "python",
+        "latex",
+        "bash",
+        "companies",
+        "softwareTerms",
+        "misc",
+        "en_US",
+        "en-gb",
+        "filetypes",
+        "neuroscience"
+    ]
+}
diff --git a/docs/cspell/neuroscience.txt b/docs/cspell/neuroscience.txt
new file mode 100644
index 00000000..2b27901f
--- /dev/null
+++ b/docs/cspell/neuroscience.txt
@@ -0,0 +1,104 @@
+*anat*
+*anthony
+*apply*
+*b0*
+*bet*
+*bore
+*bundle*
+*bval*
+*bvec*
+*coeff
+*coeffs
+*container
+*containers
+*core
+*crop*
+*denoise*
+*dwi*
+*easy*
+*extract*
+*fast*
+*field*
+*fodf*
+*frf*
+*image
+*local*
+*mask
+*mean*
+*means*
+*metrics
+*morph*
+*mov*
+*neuro*
+*normalise
+*pack
+*par
+*pft*
+*reg*
+*registration*
+*rev*
+*seg*
+*synth*
+*test*
+*to*
+*tracking*
+*transforms
+*volume*
+ants*
+aparc
+arnaud*
+aseg
+connectomics
+denoised
+denoising
+descoteaux
+dev*
+dipy
+dti*
+dtype
+etienne
+evals
+evecs
+extension*
+freesurfer*
+fsl*
+gagnon*
+interp
+medde
+mkdirs
+mppca
+mrdegibbs
+mrtrix
+msmt
+nextflow
+nf*
+nifti
+nl*
+nufo
+onge
+parcellation
+parcellations
+preproc
+reconst
+rheault
+robsyme
+sbref
+scilpy
+scilus
+seed*
+ssst
+stanislas
+subworkflow
+subworkflows
+thoumyre
+topup
+track*
+tractoflow
+tractogram
+tractograms
+tractography
+transfo
+uchar
+unbias
+wmparc
+zenodo
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/main.nf b/modules/nf-neuro/betcrop/fslbetcrop/main.nf
index 1da42ed9..54fc9ddf 100755
--- a/modules/nf-neuro/betcrop/fslbetcrop/main.nf
+++ b/modules/nf-neuro/betcrop/fslbetcrop/main.nf
@@ -69,16 +69,9 @@ process BETCROP_FSLBETCROP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    scil_dwi_extract_b0.py -h
-    bet -h
-    scil_volume_math.py -h
-    mrcalc -h
-    scil_volume_crop.py -h
-
     touch ${prefix}__image_bet.nii.gz
     touch ${prefix}__image_bet_mask.nii.gz
     touch ${prefix}__image_boundingBox.pkl
@@ -89,5 +82,18 @@ process BETCROP_FSLBETCROP {
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([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
+
+    bet
+    scil_dwi_extract_b0.py -h
+    scil_volume_math.py -h
+    mrcalc -h
+    scil_volume_crop.py -h
     """
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test
index d24c8b08..c89409da 100644
--- a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test
+++ b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test
@@ -108,4 +108,32 @@ nextflow_process {
 
     }
 
+    test("betcrop - fslbetcrop - 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}/dwi/dwi.nii.gz"),
+                        file("\${test_data_directory}/dwi/dwi.bval"),
+                        file("\${test_data_directory}/dwi/dwi.bvec")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
index 8d1977ef..47640ecb 100644
--- a/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
+++ b/modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
@@ -1,4 +1,16 @@
 {
+    "betcrop - fslbetcrop - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,cc45ab23921525536874337c1c88e5cf"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T10:33:04.50811"
+    },
     "betcrop - fslbetcrop - dwi": {
         "content": [
             {
diff --git a/modules/nf-neuro/denoising/mppca/main.nf b/modules/nf-neuro/denoising/mppca/main.nf
index dfbe9e99..4eb498d8 100755
--- a/modules/nf-neuro/denoising/mppca/main.nf
+++ b/modules/nf-neuro/denoising/mppca/main.nf
@@ -3,9 +3,7 @@ process DENOISING_MPPCA {
     tag "$meta.id"
     label 'process_medium'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
     tuple val(meta), path(dwi), path(mask)
@@ -30,13 +28,12 @@ process DENOISING_MPPCA {
     export MRTRIX_RNG_SEED=112524
 
     dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")}
-    scil_volume_math.py lower_clip ${prefix}_dwi_denoised.nii.gz 0 \
-        ${prefix}_dwi_denoised.nii.gz -f
+    mrcalc ${prefix}_dwi_denoised.nii.gz 0 -gt ${prefix}_dwi_denoised.nii.gz 0 \
+        -if ${prefix}_dwi_denoised.nii.gz -force
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -46,14 +43,13 @@ process DENOISING_MPPCA {
 
     """
     dwidenoise -h
-    scil_volume_math.py -h
+    mrcalc -h
 
     touch ${prefix}_dwi_denoised.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/denoising/mppca/meta.yml b/modules/nf-neuro/denoising/mppca/meta.yml
index 34744795..5ce90fe6 100755
--- a/modules/nf-neuro/denoising/mppca/meta.yml
+++ b/modules/nf-neuro/denoising/mppca/meta.yml
@@ -12,9 +12,6 @@ tools:
   - "MRtrix3":
       description: "Toolbox for image processing, analysis and visualisation of dMRI."
       homepage: "https://mrtrix.readthedocs.io/en/latest/"
-  - "scilpy":
-      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
-      homepage: "https://github.com/scilus/scilpy.git"
 
 input:
   - meta:
diff --git a/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
index ab3c336d..21195dd7 100644
--- a/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
+++ b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ],
                 "image": [
                     [
@@ -22,14 +22,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0-rc1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-08-05T15:17:51.718413"
+        "timestamp": "2024-12-12T18:27:14.057961679"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/image/applymask/main.nf b/modules/nf-neuro/image/applymask/main.nf
index 9332cad2..f7dc660d 100644
--- a/modules/nf-neuro/image/applymask/main.nf
+++ b/modules/nf-neuro/image/applymask/main.nf
@@ -2,9 +2,7 @@ process IMAGE_APPLYMASK {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
         tuple val(meta), path(image), path(mask)
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/gibbs/main.nf b/modules/nf-neuro/preproc/gibbs/main.nf
index 16b3d7b6..1744e5d9 100644
--- a/modules/nf-neuro/preproc/gibbs/main.nf
+++ b/modules/nf-neuro/preproc/gibbs/main.nf
@@ -2,9 +2,7 @@ process PREPROC_GIBBS {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "mrtrix3/mrtrix3:latest"
 
     input:
     tuple val(meta), path(dwi)
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",
diff --git a/poetry.lock b/poetry.lock
index 8100f7b8..185cdd26 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -2429,4 +2429,4 @@ cffi = ["cffi (>=1.11)"]
 [metadata]
 lock-version = "2.0"
 python-versions = "<3.11,>=3.9"
-content-hash = "86ff61aa15873147e59b28a6ff0b1ac405796dde631e28216829299332fdfa26"
+content-hash = "84934e125505bfaca09ac4232c63d5c53fa66696503f122fcf1feef8d306e4e8"
diff --git a/pyproject.toml b/pyproject.toml
index 155550ea..fc149a48 100755
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,3 +38,4 @@ python = "<3.11,>=3.9"
 nf-core = "~2.14.1"
 black = "^24.1.1"
 isort = "^5.13.2"
+pdiff = "^1.1.4"
diff --git a/subworkflows/nf-neuro/load_test_data/main.nf b/subworkflows/nf-neuro/load_test_data/main.nf
index 612c68a7..5a1dbcc3 100644
--- a/subworkflows/nf-neuro/load_test_data/main.nf
+++ b/subworkflows/nf-neuro/load_test_data/main.nf
@@ -1,36 +1,147 @@
-import java.nio.file.Files
 
-def fetch_archive ( name, destination, remote, database, data_identifiers ) {
-    // Find cache location for test archives
+
+def locate_local_cache () {
+    // Find cache location for test archives, in order of preference:
+    // 1. Using environment variable $NFNEURO_TEST_DATA_HOME
+    // 2. Using environment variable $XDG_DATA_HOME
+    // 3. Using default location $HOME/.local/share
+    //
+    // Location selected is appended with 'nf-neuro-test-archives'.
+    // If the location does not exist, it is created.
+
     def storage = file(
         System.getenv('NFNEURO_TEST_DATA_HOME') ?:
         System.getenv('XDG_DATA_HOME') ?:
         "${System.getenv('HOME')}/.local/share"
     )
     def cache_location = file("$storage/nf-neuro-test-archives")
-    if ( !cache_location.exists() ) cache_location.mkdirs()
 
-    // Fetch file from remote if not present in cache
-    def data_id = data_identifiers[name]
-    if ( !data_id ) {
-        error "Invalid test data identifier supplied: $name"
+    if ( !cache_location.exists() ) {
+        try {
+            cache_location.mkdirs()
+        }
+        catch (Exception _e) {
+            error "Failed to create cache location: $cache_location"
+        }
+    }
+
+    return cache_location
+}
+
+def locate_remote_cache () {
+    return "$params.test_data_remote/$params.test_database_path"
+}
+
+def load_manifest () {
+    // Load test data associations from params.test_data_associations
+    // which must be a map of test data identifiers [filename: identifier]
+
+    if ( ! params.test_data_associations ) {
+        error """
+        No test data associations provided, cannot create cache manifest. Please
+        provide a map of test data identifiers [filename: identifier] using
+        params.test_data_associations.
+        """
+    }
+
+    return params.test_data_associations
+}
+
+def validate_cache_entry ( name, manager ) {
+    // Check if the cache entry is present in the manifest
+
+    if ( !manager.manifest[name] ) {
+        error "Invalid cache entry supplied : $name"
+    }
+
+}
+
+def add_cache_entry ( name, manager ) {
+    // Add the test data archive as an entry in the cache. The archive is
+    // fetched from the remote location and stored in the cache location.
+    // The given name is validated against the manifest before adding.
+
+    manager.validate_entry(name)
+
+    def identifier = "${manager.manifest[name]}"
+    def cache_entry = file("${manager.cache_location}/$identifier")
+    def remote_subpath = "${identifier[0..1]}/${identifier[2..-1]}"
+    def remote_entry = file("$manager.remote_location/$remote_subpath")
+
+    try {
+        remote_entry.copyTo(cache_entry)
+    }
+    catch (Exception _e) {
+        manager.delete_entry(name)
+        error "Failed to fetch test data archive: $name | $_e"
     }
 
-    def cache_entry = file("$cache_location/$data_id")
-    if ( !cache_entry.exists() ) {
+    return cache_entry
+}
+
+def get_cache_entry ( name, manager ) {
+    // Retrieve the cache entry for the given test data archive name.
+    // If the entry does not exist, it is added to the cache. The add
+    // operation will validate the name against the manifest.
+
+    def identifier = "${manager.manifest[name]}"
+    def cache_entry = file("${manager.cache_location}/$identifier")
+
+    if ( !cache_entry.exists() ) manager.add_entry(name)
+
+    return cache_entry
+}
+
+def delete_cache_entry ( name, manager ) {
+    // Delete the cache entry for the given test data archive name.
+
+    def identifier = "${manager.manifest[name]}"
+    def cache_entry = file("${manager.cache_location}/$identifier")
+    if ( cache_entry.exists() ) {
         try {
-            def remote_entry = "${data_id[0..1]}/${data_id[2..-1]}"
-            file("$remote/$database/$remote_entry").copyTo(cache_entry)
+            cache_entry.delete()
         }
-        catch (Exception e) {
-            error "Failed to fetch test data archive: $name"
-            file("$remote/$database/$remote_entry").delete()
+        catch (Exception _e) {
+            error "Failed to delete test data archive: $name"
         }
     }
+}
 
+def update_cache_entry ( name, manager ) {
+    // Update the cache entry for the given test data archive name. The
+    // procedure uses add to carry the update, but deletes the entry first
+    // if it exists. The add operation will validate the name against
+    // the manifest.
+
+    manager.delete_entry(name)
+    manager.add_entry(name)
+}
+
+def setup_cache () {
+    // Build a cache manager to encapsulate interaction with the test data cache.
+    // The manager follows simple CRUD operation to handle update and retrieval of
+    // test data archives from the cache and the remote location.
+
+    def cache_manager = new Expando(
+        remote_location: locate_remote_cache(),
+        cache_location: locate_local_cache(),
+        manifest: load_manifest()
+    )
+    cache_manager.validate_entry = { v -> validate_cache_entry( v, cache_manager ) }
+    cache_manager.add_entry = { v -> add_cache_entry(v, cache_manager) }
+    cache_manager.get_entry = { v -> get_cache_entry(v, cache_manager) }
+    cache_manager.delete_entry = { v -> delete_cache_entry(v, cache_manager) }
+    cache_manager.update_entry = { v -> update_cache_entry(v, cache_manager) }
+
+    return cache_manager
+}
+
+
+def fetch_archive ( name, destination, manager ) {
     // Unzip all archive content to destination
-    def content = new java.util.zip.ZipFile("$cache_entry")
+    def content = null
     try {
+        content = new java.util.zip.ZipFile("${manager.get_entry(name)}")
         content.entries().each{ entry ->
             def local_target = file("$destination/${entry.getName()}")
             if (entry.isDirectory()) {
@@ -42,11 +153,14 @@ def fetch_archive ( name, destination, remote, database, data_identifiers ) {
                 }
             }
         }
+        content.close()
 
         return destination.resolve("${name.take(name.lastIndexOf('.'))}")
     }
-    finally {
-        content.close()
+    catch (Exception _e) {
+        if (content) content.close()
+        manager.delete_entry(name)
+        error "Failed to extract test data archive: $name | $_e"
     }
 }
 
@@ -57,16 +171,11 @@ workflow LOAD_TEST_DATA {
     test_data_prefix
 
     main:
+    manager = setup_cache()
 
-    ch_versions = Channel.empty()
-    test_data_path = Files.createTempDirectory("$test_data_prefix")
+    test_data_path = java.nio.file.Files.createTempDirectory("$test_data_prefix")
     ch_test_data_directory = ch_archive.map{ archive ->
-        fetch_archive(
-            archive, test_data_path,
-            params.test_data_remote,
-            params.test_database_path,
-            params.test_data_associations
-        )
+        fetch_archive(archive, test_data_path, manager)
     }
 
     emit:
diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
index 962db759..370fa97f 100644
--- a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
@@ -15,10 +15,10 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
+                "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
-                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
@@ -32,9 +32,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-01T12:50:45.411022164"
+        "timestamp": "2024-12-12T18:30:03.433004717"
     },
     "preproc_dwi_rev_b0": {
         "content": [
@@ -52,7 +52,7 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
@@ -68,9 +68,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-01T12:49:12.328235961"
+        "timestamp": "2024-12-12T18:28:35.975149345"
     },
     "preproc_dwi_all_options": {
         "content": [
@@ -88,10 +88,10 @@
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
                 "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
-                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
+                "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
+                "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
-                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,ea5858879452a59bb355228ae7f38111",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
@@ -107,6 +107,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-29T13:47:57.561745796"
+        "timestamp": "2024-12-12T18:31:26.492075412"
     }
 }
\ No newline at end of file
diff --git a/tests/nextflow.config b/tests/nextflow.config
index c7b2182a..77959c0a 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1,4 +1,3 @@
-import groovy.json.JsonSlurper
 
 params {
     outdir = "output/"
@@ -7,7 +6,7 @@ params {
 
     test_data_remote = "https://scil.usherbrooke.ca"
     test_database_path = "scil_test_data/dvc-store/files/md5"
-    test_data_associations = new JsonSlurper().parse(
+    test_data_associations = new groovy.json.JsonSlurper().parse(
         new File("$projectDir/tests/test_data.json")
     )
 }
diff --git a/tests/test_data.json b/tests/test_data.json
index c7a1bdb5..cd5e7f52 100644
--- a/tests/test_data.json
+++ b/tests/test_data.json
@@ -57,6 +57,5 @@
     "freesurfer_nifti.zip": "adb5ac4cf5c45040339e04e7c142e8c9",
     "transform.zip": "148afd665ddbd2bb80493208480571a9",
     "dicom.zip": "234913cbad53c19aa19aef9eda0a3839",
-    "freesurfer_nifti.zip": "adb5ac4cf5c45040339e04e7c142e8c9",
     "TOPUP.zip": "da11914087a1a4ed1d21d478540d41b0"
 }