Adjust nextflow config and output format

scilus · Apr 26, 2024 · 7608de4 · 7608de4
1 parent 2fa8c08
commit 7608de4
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Showing 4 changed files with 25 additions and 17 deletions.
diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf
@@ -11,7 +11,7 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     output:
     tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image
-    tuple val(meta), path("*__deform_warp.m3z"), 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
 
@@ -31,16 +31,13 @@ process REGISTRATION_SYNTHREGISTRATION {
     def extent = task.ext.extent ? "-e " + task.ext.extent : ""
     def weight = task.ext.weight ? "-w " + task.ext.weight : ""
 
-    //For arguments definition, mri_warp_convert -h
-    def out_format = task.ext.out_format ? "--out" + task.ext.out_format : "--outlps"
-
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
     mri_synthmorph $init -g -t ${prefix}__init_warp.lta $moving $fixed
-    mri_synthmorph $warp -g -i ${prefix}__init_warp.lta  -t ${prefix}__deform_warp.m3d -o ${prefix}__output_warped.nii.gz $moving $fixed
+    mri_synthmorph $warp -g -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}":

diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml
@@ -7,8 +7,8 @@ keywords:
   - MRI
 tools:
   - "Freesurfer":
-      description: "Freesurfer Toolbox"
-      homepage: "https://surfer.nmr.mgh.harvard.edu/"
+      description: "Freesurfer Synthmorph"
+      homepage: "https://martinos.org/malte/synthmorph/"
 
 
 input:
@@ -48,7 +48,7 @@ output:
   - deform_transform:
       type: file
       description: Deform transformation
-      pattern: "*.{m3z}"
+      pattern: "*.{nii,.nii.gz}"
 
   - warped_image:
       type: file

diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
@@ -5,8 +5,8 @@ params {
 }
 
 process {
-    cpus = 4
-    memory = 5.GB
+    cpus = 16
+    memory = 20.GB
     time = 2.h
 }
 

diff --git a/tests/modules/nf-scil/registration/synthregistration/test.yml b/tests/modules/nf-scil/registration/synthregistration/test.yml
@@ -1,11 +1,22 @@
 - 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
+    - registration/synthregistration
   files:
-    - path: "output/registration/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
-    - path: "output/registration/versions.yml"
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
-
+    - path: output/registration/test__deform_warp.nii.gz
+      md5sum: e0ed8084afa172668f50579f0585706c
+    - path: output/registration/test__init_warp.lta
+      md5sum: 4c5b29a64c8db1f87dd9ecf83a2d9878
+    - path: output/registration/test__output_warped.nii.gz
+      md5sum: 2b0441e95fd48bc269833d05831cfd9e
+    - path: output/registration/versions.yml
+    - path: output/testdata/test_data/freesurfer/anat_image.nii.gz
+      md5sum: ba57c629e9dc29204215dceac36d65ae
+    - path: output/testdata/test_data/freesurfer/fa.nii.gz
+      md5sum: 0e76e9378500de64d66ba3d787a147ca
+    - path: output/testdata/test_data/freesurfer/license.txt
+      md5sum: 3db0fa4e1860b4774c7855980e406275
+    - path: output/testdata/test_data/freesurfer/t1.nii.gz
+      md5sum: a6ade205420f594737ad67f9fb246f0f
+    - path: output/testdata/versions.yml