From d009a88f4a92b6048e3ea8a5446cc034496837b3 Mon Sep 17 00:00:00 2001
From: anroy1 <a.royer111@gmail.com>
Date: Tue, 14 May 2024 13:44:19 +0000
Subject: [PATCH] Switch transform output to fs .nii.gz format

---
 modules/nf-scil/registration/synthregistration/main.nf     | 7 +++----
 modules/nf-scil/registration/synthregistration/meta.yml    | 2 +-
 .../nf-scil/registration/synthregistration/test.yml        | 5 ++---
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
index aec53edc4..8d130b825 100644
--- a/modules/nf-scil/registration/synthregistration/main.nf
+++ b/modules/nf-scil/registration/synthregistration/main.nf
@@ -8,10 +8,9 @@ process REGISTRATION_SYNTHREGISTRATION {
     input:
     tuple val(meta), path(moving), path(fixed)
 
-
     output:
     tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image
-    tuple val(meta), path("*__deform_warp.mgz"), emit: deform_transform
+    tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform
     tuple val (meta), path("*__init_warp.lta"), emit: init_transform
     path "versions.yml"           , emit: versions
 
@@ -38,7 +37,7 @@ process REGISTRATION_SYNTHREGISTRATION {
     export OPENBLAS_NUM_THREADS=1
 
     mri_synthmorph ${init} -t ${prefix}__init_warp.lta $moving $fixed
-    mri_synthmorph ${warp} ${gpu} ${lambda} ${steps} ${extent} ${weight} -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.mgz -o ${prefix}__output_warped.nii.gz $moving $fixed
+    mri_synthmorph ${warp} ${gpu} ${lambda} ${steps} ${extent} ${weight} -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.nii.gz -o ${prefix}__output_warped.nii.gz $moving $fixed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -54,7 +53,7 @@ process REGISTRATION_SYNTHREGISTRATION {
     mri_synthmorph -h
 
     touch ${prefix}__output_warped.nii.gz
-    touch ${prefix}__deform_warp.mgz
+    touch ${prefix}__deform_warp.nii.gz
     touch ${prefix}__init_warp.lta
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
index 9a3c2de11..5fe45c454 100644
--- a/modules/nf-scil/registration/synthregistration/meta.yml
+++ b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -42,7 +42,7 @@ output:
   - deform_transform:
       type: file
       description: Deform transformation
-      pattern: "*.{mgz}"
+      pattern: "*.{nii.gz}"
 
   - warped_image:
       type: file
diff --git a/tests/modules/nf-scil/registration/synthregistration/test.yml b/tests/modules/nf-scil/registration/synthregistration/test.yml
index e19c287b7..925c6bdb8 100644
--- a/tests/modules/nf-scil/registration/synthregistration/test.yml
+++ b/tests/modules/nf-scil/registration/synthregistration/test.yml
@@ -4,9 +4,8 @@
     - registration/synthregistration
     - registration
   files:
-    - path: output/registration/test__deform_warp.mgz
-      contains:
-        - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead '
+    - path: output/registration/test__deform_warp.nii.gz
+      md5sum: d01c753043af2257908d049ade978981
     - path: output/registration/test__init_warp.lta
       md5sum: 46ad5a5d359b2ec157d1164135e746eb
     - path: output/registration/test__output_warped.nii.gz