Fix Alex's comments

scilus · Sep 25, 2024 · 99dc26a · 99dc26a
1 parent f6a0866
commit 99dc26a
Show file tree

Hide file tree

Showing 4 changed files with 29 additions and 36 deletions.
diff --git a/subworkflows/nf-neuro/anatomical_segmentation/main.nf b/subworkflows/nf-neuro/anatomical_segmentation/main.nf
@@ -1,11 +1,8 @@
 // ** Importing modules from nf-neuro ** //
 include { SEGMENTATION_FASTSEG       } from '../../../modules/nf-neuro/segmentation/fastseg/main'
 include { SEGMENTATION_FREESURFERSEG } from '../../../modules/nf-neuro/segmentation/freesurferseg/main'
-
 include { SEGMENTATION_SYNTHSEG      } from '../../../modules/nf-neuro/segmentation/synthseg/main'
 
-params.run_synthseg = params.run_synthseg ?: false
-
 workflow ANATOMICAL_SEGMENTATION {
 
     // ** Two input channels for the segmentation processes since they are using   ** //
@@ -19,10 +16,6 @@ workflow ANATOMICAL_SEGMENTATION {
 
         ch_versions = Channel.empty()
 
-        if ( ch_image && ch_freesurferseg ) {
-            error('Both input channels cannot be passed simultaneously')
-        }
-
         if ( ch_freesurferseg ) {
             // ** Freesurfer segmentation ** //
             SEGMENTATION_FREESURFERSEG ( ch_freesurferseg )
@@ -47,13 +40,13 @@ workflow ANATOMICAL_SEGMENTATION {
                 wm_mask = SEGMENTATION_SYNTHSEG.out.wm_mask
                 gm_mask = SEGMENTATION_SYNTHSEG.out.gm_mask
                 csf_mask = SEGMENTATION_SYNTHSEG.out.csf_mask
-                parc = SEGMENTATION_SYNTHSEG.out.parc
-                resample = SEGMENTATION_SYNTHSEG.out.resample
-                volume = SEGMENTATION_SYNTHSEG.out.vol
-                qc = SEGMENTATION_SYNTHSEG.out.qc
                 wm_map = Channel.empty()
                 gm_map = Channel.empty()
                 csf_map = Channel.empty()
+                gm_parc = SEGMENTATION_SYNTHSEG.out.gm_parc
+                resample = SEGMENTATION_SYNTHSEG.out.resample
+                volume = SEGMENTATION_SYNTHSEG.out.volume
+                qc_score = SEGMENTATION_SYNTHSEG.out.qc_score
             }
 
             else {
@@ -75,12 +68,13 @@ workflow ANATOMICAL_SEGMENTATION {
         wm_mask   = wm_mask                     // channel: [ val(meta), [ wm_mask ] ]
         gm_mask   = gm_mask                     // channel: [ val(meta), [ gm_mask ] ]
         csf_mask  = csf_mask                    // channel: [ val(meta), [ csf_mask ] ]
-        parc = parc                             // channel: [ val(meta), [ parc ] ]
-        resample = resample                     // channel: [ val(meta), [ resample ] ]
-        qc = qc                                 // channel: [ val(meta), [ qc ] ]
         wm_map    = wm_map                      // channel: [ val(meta), [ wm_map ] ]
         gm_map    = gm_map                      // channel: [ val(meta), [ gm_map ] ]
         csf_map   = csf_map                     // channel: [ val(meta), [ csf_map ] ]
+        gm_parc   = gm_parc                       // channel: [ val(meta), [ gm_parc ] ]
+        resample  = resample                     // channel: [ val(meta), [ resample ] ]
+        volume    = volume                         // channel: [ val(meta), [ volume ] ]
+        qc_score  = qc_score                     // channel: [ val(meta), [ qc_score ] ]
 
         versions = ch_versions                  // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-neuro/anatomical_segmentation/meta.yml b/subworkflows/nf-neuro/anatomical_segmentation/meta.yml
@@ -17,6 +17,7 @@ keywords:
 components:
   - segmentation/fastseg
   - segmentation/freesurferseg
+  - segmentation/synthseg
 input:
   - ch_image:
       type: file
@@ -62,24 +63,6 @@ output:
         is used and not with FreeSurfer's parcellation files.
         Structure: [ val(meta), path(wm_maps) ]
       pattern: "*.{nii,nii.gz}"
-  - parc:
-      type: file
-      description: |
-        Channel containing the optional nifti cortical parcellation volume from synthseg.
-        pattern: "*.{nii,nii.gz}"
-        Structure: [ val(meta), path(parc) ]
-  - vol:
-      type: file
-      description: |
-        Channel containing the optional Output CSV file with volumes for all structures and subjects.
-        Structure: [ val(meta), path(vol) ]
-      pattern: "*.csv"
-  - qc:
-      type: file
-      description: |
-        Channel containing the optional output CSV file with qc scores for all subjects.
-        Structure: [ val(meta), path(qc) ]
-      pattern: "*.csv"
   - gm_maps:
       type: file
       description: |
@@ -94,6 +77,24 @@ output:
         is used and not with FreeSurfer's parcellation files.
         Structure: [ val(meta), path(csf_maps) ]
       pattern: "*.{nii,nii.gz}"
+  - gm_parc:
+      type: file
+      description: |
+        Channel containing the optional nifti cortical parcellation volume from synthseg.
+        pattern: "*.{nii,nii.gz}"
+        Structure: [ val(meta), path(gm_parc) ]
+  - volume:
+      type: file
+      description: |
+        Channel containing the optional Output CSV file with volumes for all structures and subjects.
+        Structure: [ val(meta), path(volume) ]
+      pattern: "*.csv"
+  - qc_score:
+      type: file
+      description: |
+        Channel containing the optional output CSV file with qc scores for all subjects.
+        Structure: [ val(meta), path(qc_score) ]
+      pattern: "*.csv"
   - versions:
       type: file
       description: |

diff --git a/subworkflows/nf-neuro/anatomical_segmentation/tests/main.nf.test b/subworkflows/nf-neuro/anatomical_segmentation/tests/main.nf.test
@@ -11,6 +11,7 @@ nextflow_workflow {
     tag "segmentation"
     tag "segmentation/fastseg"
     tag "segmentation/freesurferseg"
+    tag "segmentation/synthseg"
 
     tag "load_test_data"
 

diff --git a/subworkflows/nf-neuro/anatomical_segmentation/tests/nextflow_synthseg.config b/subworkflows/nf-neuro/anatomical_segmentation/tests/nextflow_synthseg.config
@@ -3,9 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     withName: "REGISTRATION_SYNTHSEG" {
         ext.fast = true
+        run_synthseg = true
     }
 }
-
-params {
-    run_synthseg = true
-}