Fix Alex's comments

scilus · Sep 24, 2024 · 0eff8dc · 0eff8dc
1 parent 9820646
commit 0eff8dc
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Showing 4 changed files with 35 additions and 38 deletions.
diff --git a/modules/nf-neuro/registration/convert/environment.yml b/modules/nf-neuro/registration/convert/environment.yml
@@ -1,7 +1,3 @@
----
-name: "registration_convert"
-channels:
-  - Docker
-  - Apptainer
-dependencies:
-  - "Freesurfer"
+channels: []
+dependencies: []
+name: registration_convert
diff --git a/modules/nf-neuro/registration/convert/main.nf b/modules/nf-neuro/registration/convert/main.nf
@@ -10,7 +10,7 @@ process REGISTRATION_CONVERT {
     tuple val(meta), path(affine), path(deform), path(source), path(target) /* optional, value = [] */, path(fs_license) /* optional, value = [] */
 
     output:
-    tuple val(meta), path("*.{txt,lta,mat,dat}"), emit: init_transform
+    tuple val(meta), path("*.{txt,lta,mat,dat}"), emit: affine_transform
     tuple val(meta), path("*.{nii,nii.gz,mgz,m3z}"), emit: deform_transform
     path "versions.yml"           , emit: versions
 

diff --git a/modules/nf-neuro/registration/convert/meta.yml b/modules/nf-neuro/registration/convert/meta.yml
@@ -1,10 +1,11 @@
 ---
 name: "registration_convert"
-description: Freesurfer transform conversion tool. Default usage is aim at receiving freesurfer format and converting to ANTs (ITK). See lta_convert --help and mri_warp_convert --help for alternatives.
+description: Freesurfer transform conversion tool. Default usage is aim at receiving freesurfer format and converting to ANTs (ITK). See lta_convert --help and mri_warp_convert --help for options.
 keywords:
   - Registration
   - Brain imaging
   - MRI
+  - Conversion
 tools:
   - "Freesurfer":
       description: "Freesurfer lta_convert (affine conversion) and mri_warp_convert (deform) tools for transform conversion"
@@ -50,9 +51,9 @@ output:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - init_transform:
+  - affine_transform:
       type: file
-      description: Init transform. Default usage outputs ANTs (ITK) format .txt
+      description: Affine transform. Default usage outputs ANTs (ITK) format .txt
       pattern: "*.{txt,lta,mat,dat}"
 
   - deform_transform:

diff --git a/modules/nf-neuro/registration/convert/tests/main.nf.test.snap b/modules/nf-neuro/registration/convert/tests/main.nf.test.snap
@@ -21,20 +21,20 @@
                 "2": [
                     "versions.yml:md5,9912ec095965c1ff571f77b447c18f92"
                 ],
-                "deform_transform": [
+                "affine_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__deform_warp.nii.gz:md5,69052e6226da946bad1f9466285cbb89"
+                        "test__init_warp.txt:md5,5f989a979be61faa578ad619377a8a07"
                     ]
                 ],
-                "init_transform": [
+                "deform_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__init_warp.txt:md5,5f989a979be61faa578ad619377a8a07"
+                        "test__deform_warp.nii.gz:md5,69052e6226da946bad1f9466285cbb89"
                     ]
                 ],
                 "versions": [
@@ -46,7 +46,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T13:35:37.562833"
+        "timestamp": "2024-09-24T19:51:31.308519"
     },
     "registration - convert - default": {
         "content": [
@@ -70,20 +70,20 @@
                 "2": [
                     "versions.yml:md5,9912ec095965c1ff571f77b447c18f92"
                 ],
-                "deform_transform": [
+                "affine_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__deform_warp.nii.gz:md5,69052e6226da946bad1f9466285cbb89"
+                        "test__init_warp.txt:md5,5f989a979be61faa578ad619377a8a07"
                     ]
                 ],
-                "init_transform": [
+                "deform_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__init_warp.txt:md5,5f989a979be61faa578ad619377a8a07"
+                        "test__deform_warp.nii.gz:md5,69052e6226da946bad1f9466285cbb89"
                     ]
                 ],
                 "versions": [
@@ -95,7 +95,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T13:35:31.823233"
+        "timestamp": "2024-09-24T19:51:26.803266"
     },
     "registration - convert - antsfs": {
         "content": [
@@ -105,7 +105,7 @@
                         {
                             "id": "test"
                         },
-                        "test__init_warp.lta:md5,12c3608398da5039c99173160c1dc1a0"
+                        "test__init_warp.lta:md5,d3afe0fa6944ead0c7289bcbcda104e2"
                     ]
                 ],
                 "1": [
@@ -119,20 +119,20 @@
                 "2": [
                     "versions.yml:md5,9912ec095965c1ff571f77b447c18f92"
                 ],
-                "deform_transform": [
+                "affine_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__deform_warp.nii.gz:md5,599fbe3a6b85d61c0c67cea8be4972b7"
+                        "test__init_warp.lta:md5,d3afe0fa6944ead0c7289bcbcda104e2"
                     ]
                 ],
-                "init_transform": [
+                "deform_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__init_warp.lta:md5,12c3608398da5039c99173160c1dc1a0"
+                        "test__deform_warp.nii.gz:md5,599fbe3a6b85d61c0c67cea8be4972b7"
                     ]
                 ],
                 "versions": [
@@ -144,7 +144,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T13:36:08.620317"
+        "timestamp": "2024-09-24T19:52:03.847929"
     },
     "registration - convert - fslants": {
         "content": [
@@ -168,20 +168,20 @@
                 "2": [
                     "versions.yml:md5,9912ec095965c1ff571f77b447c18f92"
                 ],
-                "deform_transform": [
+                "affine_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__deform_warp.nii.gz:md5,94feb8f0e648256eaa5ae0a47e5702c6"
+                        "test__init_warp.txt:md5,074e8ac5777a91ba0808cd58c5a0cc44"
                     ]
                 ],
-                "init_transform": [
+                "deform_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__init_warp.txt:md5,074e8ac5777a91ba0808cd58c5a0cc44"
+                        "test__deform_warp.nii.gz:md5,94feb8f0e648256eaa5ae0a47e5702c6"
                     ]
                 ],
                 "versions": [
@@ -193,7 +193,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T13:36:03.894093"
+        "timestamp": "2024-09-24T19:51:59.053418"
     },
     "registration - convert - fslfs": {
         "content": [
@@ -203,7 +203,7 @@
                         {
                             "id": "test"
                         },
-                        "test__init_warp.lta:md5,de6b45f72c3fcec98c3cd1ab97967154"
+                        "test__init_warp.lta:md5,98fae3bce7cfc2ba2383c9d120d38dcd"
                     ]
                 ],
                 "1": [
@@ -217,20 +217,20 @@
                 "2": [
                     "versions.yml:md5,9912ec095965c1ff571f77b447c18f92"
                 ],
-                "deform_transform": [
+                "affine_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__deform_warp.nii.gz:md5,df432a27c586e57cad93af7509941cd4"
+                        "test__init_warp.lta:md5,98fae3bce7cfc2ba2383c9d120d38dcd"
                     ]
                 ],
-                "init_transform": [
+                "deform_transform": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__init_warp.lta:md5,de6b45f72c3fcec98c3cd1ab97967154"
+                        "test__deform_warp.nii.gz:md5,df432a27c586e57cad93af7509941cd4"
                     ]
                 ],
                 "versions": [
@@ -242,6 +242,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-24T13:35:50.821192"
+        "timestamp": "2024-09-24T19:51:45.41656"
     }
 }