From 670aa0fec0bc95159bda8d8bdcf4b165fc504c77 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Tue, 13 Jan 2026 16:47:09 +0100
Subject: [PATCH 1/2] fix _filesin main.nf + update local tracking

---
 main.nf                                       |  2 +-
 modules.json                                  |  2 +-
 .../nf-neuro/tracking/localtracking/main.nf   | 22 +++++++++++++++++--
 .../nf-neuro/tracking/localtracking/meta.yml  |  4 ++++
 .../localtracking/tests/main.nf.test.snap     |  8 +++----
 .../localtracking/tests/nextflow_fa.config    |  2 +-
 6 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index c486cbe..12a38c4 100644
--- a/main.nf
+++ b/main.nf
@@ -88,7 +88,7 @@ workflow {
         }
     }
     else {
-        ch_after_preqc = ch_dwi_bvalbvec.dwi
+        ch_after_preqc = ch_dwi_bvalbvec.dwi_files
         bvs_after_preqc = ch_dwi_bvalbvec.bvs
     }
 
diff --git a/modules.json b/modules.json
index fcbe6e0..76d7c2d 100644
--- a/modules.json
+++ b/modules.json
@@ -58,7 +58,7 @@
           },
           "tracking/localtracking": {
             "branch": "main",
-            "git_sha": "b21f41f92e1ee439300b7060fc0296b56c6511b9",
+            "git_sha": "ec4f04fd25e3167ba495094925027248722c1aad",
             "installed_by": ["modules"]
           },
           "utils/extractb0": {
diff --git a/modules/nf-neuro/tracking/localtracking/main.nf b/modules/nf-neuro/tracking/localtracking/main.nf
index fe3d5ec..66058b8 100644
--- a/modules/nf-neuro/tracking/localtracking/main.nf
+++ b/modules/nf-neuro/tracking/localtracking/main.nf
@@ -31,6 +31,7 @@ process TRACKING_LOCALTRACKING {
     def local_seeding_mask = task.ext.local_seeding_mask_type ?: "wm"
 
     def local_step = task.ext.local_step ? "--step " + task.ext.local_step : ""
+    def local_step_pct = task.ext.local_step_pct ? task.ext.local_step_pct : ""
     def local_random_seed = task.ext.local_random_seed ? "--seed " + task.ext.local_random_seed : ""
     def local_seeding = task.ext.local_seeding ? "--" + task.ext.local_seeding : ""
     def local_nbr_seeds = task.ext.local_nbr_seeds ? "" + task.ext.local_nbr_seeds : ""
@@ -47,11 +48,28 @@ process TRACKING_LOCALTRACKING {
 
     def run_qc = task.ext.run_qc ? task.ext.run_qc : false
 
+    if (local_step && local_step_pct) {
+        log.warn "Both local_step and local_step_pct are set for ${meta.id}. local_step will take priority and local_step_pct will be ignored."
+    }
+
     """
+    # Set home directory. This is problematic if the container is run
+    # with non-root user which does not create a home directory. When
+    # running the local tracking using GPU, its trying to write to
+    # ~/.cache/ directory, causing the job to fail.
+    mkdir -p /tmp
+    export HOME=/tmp
+
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
+    local_step_size="$local_step"
+    if [[ -z "$local_step" ]] && [[ -n "$local_step_pct" ]]; then
+        pixdim=\$(scil_header_print_info $wm --keys pixdim | tr -d '[]' | awk '{for(i=2;i<=4;i++) if(\$i>0 && (\$i<min || min=="")) min=\$i} END {print min}')
+        local_step_size=\$(awk -v pixdim="\$pixdim" -v pct="$local_step_pct" 'BEGIN {printf "--step %.6f", pixdim * pct / 100}')
+    fi
+
     if [ "${local_tracking_mask}" == "wm" ]; then
         scil_volume_math lower_threshold $wm \
             $local_wm_tracking_mask_threshold \
@@ -83,7 +101,7 @@ process TRACKING_LOCALTRACKING {
     scil_tracking_local $fodf ${prefix}__local_seeding_mask.nii.gz \
             ${prefix}__local_tracking_mask.nii.gz tmp.trk $enable_gpu\
             $local_algo $local_seeding $local_nbr_seeds\
-            $local_random_seed $local_step $local_theta\
+            $local_random_seed \$local_step_size $local_theta\
             $local_sfthres $local_min_len\
             $local_max_len $compress $basis -f
 
@@ -102,7 +120,7 @@ process TRACKING_LOCALTRACKING {
     "random_seed": $task.ext.local_random_seed,
     "is_compress": "${task.ext.local_compress_streamlines}",
     "compress_value": $task.ext.local_compress_value,
-    "step": $task.ext.local_step,
+    "step": \${local_step_size/--step /},
     "theta": $task.ext.local_theta,
     "sfthres": $task.ext.local_sfthres,
     "min_len": $task.ext.local_min_len,
diff --git a/modules/nf-neuro/tracking/localtracking/meta.yml b/modules/nf-neuro/tracking/localtracking/meta.yml
index 78ebf54..1ccc835 100644
--- a/modules/nf-neuro/tracking/localtracking/meta.yml
+++ b/modules/nf-neuro/tracking/localtracking/meta.yml
@@ -50,6 +50,10 @@ args:
       type: float
       default: 0.5
       description: Tracking Step size.
+  - local_step_pct:
+      type: float
+      default: None
+      description: Define the step size as a percentage of the minimum voxel dimension.
   - local_random_seed:
       type: int
       default: 0
diff --git a/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap b/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap
index 2d10fbc..2837b92 100644
--- a/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap
+++ b/modules/nf-neuro/tracking/localtracking/tests/main.nf.test.snap
@@ -60,7 +60,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test__local_tracking_config.json:md5,a082f8d2f2b92cb3f2912a796942a786"
+                    "test__local_tracking_config.json:md5,6b2210436b4008b80969d2f08d0f0b68"
                 ]
             ],
             [
@@ -86,9 +86,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-22T22:40:54.584018789"
+        "timestamp": "2025-11-20T05:37:36.463253726"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/tracking/localtracking/tests/nextflow_fa.config b/modules/nf-neuro/tracking/localtracking/tests/nextflow_fa.config
index ba45d25..9cc3036 100644
--- a/modules/nf-neuro/tracking/localtracking/tests/nextflow_fa.config
+++ b/modules/nf-neuro/tracking/localtracking/tests/nextflow_fa.config
@@ -8,7 +8,7 @@ process {
         ext.local_algo = "prob"
         ext.local_seeding = "nt"
         ext.local_nbr_seeds = 100
-        ext.local_step = 1.0
+        ext.local_step_pct = 50
         ext.local_seeding_mask_type = "fa"
         ext.local_tracking_mask_type = "fa"
         ext.local_theta = 20

From e4ffb297a2233b6db5b4c0324c717ccc1f3ce454 Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Wed, 14 Jan 2026 09:15:19 +0100
Subject: [PATCH 2/2] fix ch_dwi_bvalbvec

---
 main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.nf b/main.nf
index 47ab44a..794cb3b 100644
--- a/main.nf
+++ b/main.nf
@@ -93,8 +93,8 @@ workflow {
         }
     }
     else {
-        ch_after_preqc = ch_dwi_bvalbvec.dwi_files
-        bvs_after_preqc = ch_dwi_bvalbvec.bvs
+        ch_after_preqc = ch_dwi_bvalbvec.dwi
+        bvs_after_preqc = ch_dwi_bvalbvec.bvs_files
     }
 
     if (params.run_denoising){