Merge pull request #78 from Manonedde/fix_betcropvolume

#45 - Change category cropvolume module (move to image) [WIP]

modules/nf-neuro/betcrop/cropvolume/environment.yml → modules/nf-neuro/image/cropvolume/environment.yml

@@ -1,3 +1,3 @@
 channels: []
 dependencies: []
-name: betcrop_cropvolume
+name: image_cropvolume

modules/nf-neuro/betcrop/cropvolume/main.nf → modules/nf-neuro/image/cropvolume/main.nf

@@ -1,5 +1,5 @@
 
-process BETCROP_CROPVOLUME {
+process IMAGE_CROPVOLUME {
     tag "$meta.id"
     label 'process_single'
 

modules/nf-neuro/betcrop/cropvolume/meta.yml → modules/nf-neuro/image/cropvolume/meta.yml

@@ -1,6 +1,6 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
-name: "betcrop_cropvolume"
+name: "image_cropvolume"
 description: Crop empty planes around the data in a volume
 keywords:
   - nifti

modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test → modules/nf-neuro/image/cropvolume/tests/main.nf.test

@@ -1,14 +1,14 @@
 nextflow_process {
 
-    name "Test Process BETCROP_CROPVOLUME"
+    name "Test Process IMAGE_CROPVOLUME"
     script "../main.nf"
-    process "BETCROP_CROPVOLUME"
+    process "IMAGE_CROPVOLUME"
     config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
-    tag "betcrop"
-    tag "betcrop/cropvolume"
+    tag "image"
+    tag "image/cropvolume"
 
     tag "subworkflows"
     tag "subworkflows/load_test_data"
@@ -25,7 +25,7 @@ nextflow_process {
         }
     }
 
-    test("betcrop - cropvolume") {
+    test("image - cropvolume") {
 
         when {
             process {
@@ -50,7 +50,7 @@ nextflow_process {
 
     }
 
-    test("betcrop - cropvolume - outputbbox") {
+    test("image - cropvolume - outputbbox") {
 
         config "./nextflow_bbox.config"
 

modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test.snap → modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap

@@ -1,5 +1,5 @@
 {
-    "betcrop - cropvolume - outputbbox": {
+    "image - cropvolume": {
         "content": [
             {
                 "0": [
@@ -12,25 +12,13 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
-                    ]
+
                 ],
                 "2": [
-                    "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
                 ],
                 "bounding_box": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
-                    ]
+
                 ],
                 "image": [
                     [
@@ -42,17 +30,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-28T19:30:09.320626173"
+        "timestamp": "2024-12-12T18:59:41.317523464"
     },
-    "betcrop - cropvolume": {
+    "image - cropvolume - outputbbox": {
         "content": [
             {
                 "0": [
@@ -65,13 +53,25 @@
                     ]
                 ],
                 "1": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
+                    ]
                 ],
                 "2": [
-                    "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
                 ],
                 "bounding_box": [
-
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
+                    ]
                 ],
                 "image": [
                     [
@@ -83,14 +83,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f"
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-28T19:30:00.033087617"
+        "timestamp": "2024-12-12T18:59:50.080977383"
     }
 }

modules/nf-neuro/betcrop/cropvolume/tests/nextflow.config → modules/nf-neuro/image/cropvolume/tests/nextflow.config

@@ -1,5 +1,5 @@
 process {
-    withName: "BETCROP_CROPVOLUME" {
+    withName: "IMAGE_CROPVOLUME" {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     }
 }

modules/nf-neuro/betcrop/cropvolume/tests/nextflow_bbox.config → modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config

@@ -1,5 +1,5 @@
 process {
-    withName: "BETCROP_CROPVOLUME" {
+    withName: "IMAGE_CROPVOLUME" {
         ext.output_bbox = true
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     }

modules/nf-neuro/image/cropvolume/tests/tags.yml

@@ -0,0 +1,2 @@
+image/cropvolume:
+  - "modules/nf-neuro/image/cropvolume/**"

subworkflows/nf-neuro/preproc_dwi/main.nf

@@ -1,7 +1,7 @@
 include { DENOISING_MPPCA as DENOISE_DWI } from '../../../modules/nf-neuro/denoising/mppca/main'
 include { DENOISING_MPPCA as DENOISE_REVDWI } from '../../../modules/nf-neuro/denoising/mppca/main'
 include { BETCROP_FSLBETCROP } from '../../../modules/nf-neuro/betcrop/fslbetcrop/main'
-include { BETCROP_CROPVOLUME } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
+include { IMAGE_CROPVOLUME } from '../../../modules/nf-neuro/image/cropvolume/main'
 include { PREPROC_N4 as N4_DWI } from '../../../modules/nf-neuro/preproc/n4/main'
 include { PREPROC_NORMALIZE as NORMALIZE_DWI } from '../../../modules/nf-neuro/preproc/normalize/main'
 include { IMAGE_RESAMPLE as RESAMPLE_DWI } from '../../../modules/nf-neuro/image/resample/main'
@@ -78,12 +78,12 @@ workflow PREPROC_DWI {
         ch_crop_b0 = TOPUP_EDDY.out.b0
             .join(BETCROP_FSLBETCROP.out.bbox)
 
-        BETCROP_CROPVOLUME ( ch_crop_b0 )
-        ch_versions = ch_versions.mix(BETCROP_CROPVOLUME.out.versions.first())
+        IMAGE_CROPVOLUME ( ch_crop_b0 )
+        ch_versions = ch_versions.mix(IMAGE_CROPVOLUME.out.versions.first())
 
         // ** N4 DWI ** //
         ch_N4 = BETCROP_FSLBETCROP.out.image
-            .join(BETCROP_CROPVOLUME.out.image)
+            .join(IMAGE_CROPVOLUME.out.image)
             .join(BETCROP_FSLBETCROP.out.mask)
 
         N4_DWI ( ch_N4 )

subworkflows/nf-neuro/preproc_dwi/meta.yml

@@ -45,7 +45,7 @@ keywords:
   - Normalization
   - Resampling
 components:
-  - betcrop/cropvolume
+  - image/cropvolume
   - betcrop/fslbetcrop
   - denoising/mppca
   - image/resample

subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test

@@ -9,7 +9,7 @@ nextflow_workflow {
     tag "subworkflows_nfcore"
     tag "subworkflows/preproc_dwi"
     tag "subworkflows/topup_eddy"
-    tag "betcrop/cropvolume"
+    tag "image/cropvolume"
     tag "betcrop/fslbetcrop"
     tag "denoising/mppca"
     tag "image/resample"

subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap

@@ -14,7 +14,7 @@
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
-                "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
+                "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9",
                 "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
                 "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
@@ -51,7 +51,7 @@
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
-                "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
+                "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9",
                 "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
@@ -87,7 +87,7 @@
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
                 "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b",
                 "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24",
-                "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322",
+                "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9",
                 "versions.yml:md5,571265e710ca29198e69be22c0f970d5",
                 "versions.yml:md5,662ea558da42564a0f6140473132bcb4",
                 "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7",
@@ -109,4 +109,4 @@
         },
         "timestamp": "2024-12-12T18:31:26.492075412"
     }
-}
+}

subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config

@@ -41,7 +41,7 @@ process {
         ext.voxel_size = 1
         ext.interp = "lin"
     }
-    withName: "BETCROP_CROPVOLUME" {
+    withName: "IMAGE_CROPVOLUME" {
         ext.output_bbox = false
     }
 

subworkflows/nf-neuro/preproc_t1/main.nf

@@ -4,8 +4,8 @@ include { PREPROC_N4 } from '../../../modules/nf-neuro/preproc/n4/main'
 include { IMAGE_RESAMPLE } from '../../../modules/nf-neuro/image/resample/main'
 include { BETCROP_ANTSBET } from '../../../modules/nf-neuro/betcrop/antsbet/main'
 include { BETCROP_SYNTHBET} from '../../../modules/nf-neuro/betcrop/synthbet/main'
-include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
-include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-neuro/betcrop/cropvolume/main'
+include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_T1 } from '../../../modules/nf-neuro/image/cropvolume/main'
+include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_MASK } from '../../../modules/nf-neuro/image/cropvolume/main'
 
 params.run_synthbet = false
 
@@ -126,18 +126,18 @@ workflow PREPROC_T1 {
             ch_crop = image_bet
                 .map{ it + [[]] }
 
-            BETCROP_CROPVOLUME_T1 ( ch_crop )
-            ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())
-            image_crop = BETCROP_CROPVOLUME_T1.out.image
-            bbox = BETCROP_CROPVOLUME_T1.out.bounding_box
+            IMAGE_CROPVOLUME_T1 ( ch_crop )
+            ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_T1.out.versions.first())
+            image_crop = IMAGE_CROPVOLUME_T1.out.image
+            bbox = IMAGE_CROPVOLUME_T1.out.bounding_box
 
             // ** Crop mask ** //
             ch_crop_mask = mask_bet
-                .join(BETCROP_CROPVOLUME_T1.out.bounding_box)
+                .join(IMAGE_CROPVOLUME_T1.out.bounding_box)
 
-            BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
-            ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())
-            mask_crop = BETCROP_CROPVOLUME_MASK.out.image
+            IMAGE_CROPVOLUME_MASK ( ch_crop_mask )
+            ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_MASK.out.versions.first())
+            mask_crop = IMAGE_CROPVOLUME_MASK.out.image
         }
         else{
             image_crop = image_bet

subworkflows/nf-neuro/preproc_t1/meta.yml

@@ -45,7 +45,7 @@ components:
   - image/resample
   - betcrop/antsbet
   - betcrop/synthbet
-  - betcrop/cropvolume
+  - image/cropvolume
 
 input:
   - ch_image:

subworkflows/nf-neuro/preproc_t1/tests/main.nf.test

@@ -13,7 +13,7 @@ nextflow_workflow {
     tag "image/resample"
     tag "betcrop/antsbet"
     tag "betcrop/synthbet"
-    tag "betcrop/cropvolume"
+    tag "image/cropvolume"
 
     tag "load_test_data"