From b711d52e5b7ee70b66e73582604ab8c9a0a9cb4e Mon Sep 17 00:00:00 2001
From: anroy1 <a.royer111@gmail.com>
Date: Thu, 9 May 2024 18:16:20 +0000
Subject: [PATCH] Remove license as module do not require it and update
 parameters with newer version

---
 .../nf-scil/registration/synthregistration/main.nf  | 13 +++++++------
 .../nf-scil/registration/synthregistration/meta.yml |  5 -----
 .../nf-scil/registration/synthregistration/main.nf  |  3 +--
 .../registration/synthregistration/nextflow.config  |  8 ++++++++
 .../nf-scil/registration/synthregistration/test.yml | 11 ++++++-----
 5 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
index 1131c3019..aec53edc4 100644
--- a/modules/nf-scil/registration/synthregistration/main.nf
+++ b/modules/nf-scil/registration/synthregistration/main.nf
@@ -6,7 +6,7 @@ process REGISTRATION_SYNTHREGISTRATION {
     containerOptions "--entrypoint ''"
 
     input:
-    tuple val(meta), path(moving), path(fixed), path(fs_license) /* optional, value = [] */
+    tuple val(meta), path(moving), path(fixed)
 
 
     output:
@@ -22,12 +22,13 @@ process REGISTRATION_SYNTHREGISTRATION {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def init = task.ext.init ? "-m " + task.est.init : "-m affine"
-    def warp = task.ext.warp ? "-m " + task.est.warp : "-m deform"
+    def init = task.ext.init ? "-m " + task.ext.init : "-m affine"
+    def warp = task.ext.warp ? "-m " + task.ext.warp : "-m deform"
     def header = task.ext.header ? "-H" : ""
     def threads = task.ext.threads ? "-j " + task.ext.threads : ""
     def gpu = task.ext.gpu ? "-g" : ""
-    def smooth = task.ext.smooth ? "-s " + task.ext.smooth : ""
+    def lambda = task.ext.lambda ? "-r " + task.ext.lambda : ""
+    def steps = task.ext.steps ? "-n " + task.ext.steps : ""
     def extent = task.ext.extent ? "-e " + task.ext.extent : ""
     def weight = task.ext.weight ? "-w " + task.ext.weight : ""
 
@@ -36,8 +37,8 @@ process REGISTRATION_SYNTHREGISTRATION {
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
-    mri_synthmorph $init -t ${prefix}__init_warp.lta $moving $fixed
-    mri_synthmorph $warp $gpu $smooth $extent $weight -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.mgz -o ${prefix}__output_warped.nii.gz $moving $fixed
+    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
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
index 5d3631970..9a3c2de11 100644
--- a/modules/nf-scil/registration/synthregistration/meta.yml
+++ b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -27,11 +27,6 @@ input:
       description: Nifti volume fixed for registration
       pattern: "*.{nii,nii.gz}"
 
-  - fs_license:
-      type: file
-      description: The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.
-      pattern: "*.txt"
-
 output:
   - meta:
       type: map
diff --git a/tests/modules/nf-scil/registration/synthregistration/main.nf b/tests/modules/nf-scil/registration/synthregistration/main.nf
index c45a7bd24..89f5d379f 100644
--- a/tests/modules/nf-scil/registration/synthregistration/main.nf
+++ b/tests/modules/nf-scil/registration/synthregistration/main.nf
@@ -15,8 +15,7 @@ workflow test_registration_synthregistration {
         .map{ test_data_directory -> [
         [ id:'test', single_end:false ], // meta map
         file("${test_data_directory}/t1.nii.gz"),
-        file("${test_data_directory}/fa.nii.gz"),
-        file("${test_data_directory}/license.txt")
+        file("${test_data_directory}/fa.nii.gz")
 
     ]}
 
diff --git a/tests/modules/nf-scil/registration/synthregistration/nextflow.config b/tests/modules/nf-scil/registration/synthregistration/nextflow.config
index 8730f1c4b..2a1c92753 100644
--- a/tests/modules/nf-scil/registration/synthregistration/nextflow.config
+++ b/tests/modules/nf-scil/registration/synthregistration/nextflow.config
@@ -2,4 +2,12 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: "test_registration_synthregistration:REGISTRATION_SYNTHREGISTRATION" {
+        ext.init = "affine"
+        ext.warp = "deform"
+        ext.threads = 1
+        ext.lambda = 0.5
+        ext.steps = 5
+    }
+
 }
diff --git a/tests/modules/nf-scil/registration/synthregistration/test.yml b/tests/modules/nf-scil/registration/synthregistration/test.yml
index c99172969..e19c287b7 100644
--- a/tests/modules/nf-scil/registration/synthregistration/test.yml
+++ b/tests/modules/nf-scil/registration/synthregistration/test.yml
@@ -1,15 +1,16 @@
 - name: registration synthregistration test_registration_synthregistration
   command: nextflow run ./tests/modules/nf-scil/registration/synthregistration -entry test_registration_synthregistration -c ./tests/config/nextflow.config
   tags:
-    - registration
     - registration/synthregistration
+    - registration
   files:
-    - path: output/registration/test__deform_warp.nii.gz
-      md5sum: e0ed8084afa172668f50579f0585706c
+    - 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__init_warp.lta
-      md5sum: 4c5b29a64c8db1f87dd9ecf83a2d9878
+      md5sum: 46ad5a5d359b2ec157d1164135e746eb
     - path: output/registration/test__output_warped.nii.gz
-      md5sum: 2b0441e95fd48bc269833d05831cfd9e
+      md5sum: bdc4ff1557093fd25a760e4db48d7d58
     - path: output/registration/versions.yml
     - path: output/testdata/test_data/freesurfer/anat_image.nii.gz
       md5sum: ba57c629e9dc29204215dceac36d65ae