From a7b6b6ded4b176aeefb4477e443cfaa009248f8c Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 12 Dec 2025 19:07:03 +0100
Subject: [PATCH 1/3] fodf optional step

---
 main.nf         | 3 ++-
 nextflow.config | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 6eeea69..b0207c1 100644
--- a/main.nf
+++ b/main.nf
@@ -167,6 +167,7 @@ workflow {
     ch_multiqc_files = ch_multiqc_files.mix(RECONST_DTIMETRICS.out.mqc)
 
     /* FODF */ 
+    if ( params.run_fodf ) {
     RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
     ch_for_reconst_fodf = ch_for_reconst
                             .join(RECONST_DTIMETRICS.out.fa)
@@ -174,7 +175,7 @@ workflow {
                             .join(RECONST_FRF.out.frf)
                             .map{ it + [[], []]}
     RECONST_FODF(ch_for_reconst_fodf)
-
+    }
     /* QBALL */
     RECONST_QBALL(ch_for_reconst)
 
diff --git a/nextflow.config b/nextflow.config
index edfcbf9..b92e2f2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -28,6 +28,7 @@ params {
     nvox_min = 100
 
     // FODF || QBALL
+    run_fodf = true
     use_fodf_for_tracking = false
     sh_order = 6
     min_fodf_value = 1000

From 24ffd3667259c91509b654722b5d80de4b9bd0bc Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Fri, 12 Dec 2025 22:45:30 +0000
Subject: [PATCH 2/3] add sentence

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

diff --git a/main.nf b/main.nf
index b0207c1..e70b7a1 100644
--- a/main.nf
+++ b/main.nf
@@ -68,6 +68,10 @@ workflow {
     if ( params.use_fodf_for_tracking && ! params.run_tracking ) {
         error "The parameter use_fodf_for_tracking cannot be enabled if run_tracking is disabled."
     }
+    
+    if ( params.use_fodf_for_tracking && ! params.run_fodf) {
+        error "The parameter use_fodf_for_tracking cannot be enabled if run_fodf is disabled."
+    }
 
     ch_dwi_bvalbvec = data.dwi
         .multiMap { meta, dwi, bval, bvec ->

From 7516cb4c582f0af4f185614b761fde69d1afb2ba Mon Sep 17 00:00:00 2001
From: EliseCos <elise.cosenza@u-bordeaux.fr>
Date: Sat, 13 Dec 2025 20:26:48 +0000
Subject: [PATCH 3/3] Update file nextflow_schema.json

---
 nextflow_schema.json | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1d8eece..379de8d 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -90,6 +90,12 @@
                     "description": "Set it to false if you don't want to resample your data to the smallest current voxel dimension.",
                     "fa_icon": "fas fa-brain"
                 },
+                "run_fodf": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Set it to false if you don't want to run fODF",
+                    "fa_icon": "fas fa-brain"
+                },
                 "run_tracking": {
                     "type": "boolean",
                     "default": true,