From f02fefe9fcf02d4b4b85a703223998d456d03327 Mon Sep 17 00:00:00 2001
From: anroy1 <a.royer111@gmail.com>
Date: Fri, 26 Jan 2024 12:48:18 -0500
Subject: [PATCH] test fix 1

---
 .../nf-scil/registration/synthregistration/main.nf    |  8 ++++----
 .../nf-scil/registration/synthregistration/meta.yml   | 11 ++++++++---
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
index e200f652d..81568c2bc 100644
--- a/modules/nf-scil/registration/synthregistration/main.nf
+++ b/modules/nf-scil/registration/synthregistration/main.nf
@@ -3,8 +3,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
-        'scilus/scilus:1.6.0' }"
+        'freesurfer/synthmorph:latest':
+        'freesurfer/synthmorph:latest' }"
 
     input:
     tuple val(meta), path(moving), path(fixed)
@@ -13,11 +13,11 @@ process REGISTRATION_SYNTHREGISTRATION {
     output:
     tuple val(meta), path("*__*_output_warped.nii.gz"), emit: warped_image
     tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform
-    tuple val (meta), path("*__init_warp.txt"), emit: affine_transform
+    tuple val (meta), path("*__init_warp.txt"), emit: init_transform
     path "versions.yml"           , emit: versions
 
     when:
-    task.ext.when == null || task.ext.when_output_warped
+    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
index dcfa056f1..20b738314 100644
--- a/modules/nf-scil/registration/synthregistration/meta.yml
+++ b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -35,16 +35,21 @@ output:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - init:
+  - init_transform:
       type: file
       description: Affine transform for initialization
       pattern: "*.{txt}"
 
-  - deform:
+  - deform_transform:
       type: file
       description: Deform transformation
       pattern: "*.{nii,.nii.gz}"
-  
+
+  - warped_image:
+      type: file
+      description: Warped image
+      pattern: "*.{nii,.nii.gz}"
+
   - versions:
       type: file
       description: File containing software versions