fix copy paste error

scilus · Sep 24, 2024 · 77a3ffa · 77a3ffa
1 parent eee93dc
commit 77a3ffa
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Showing 3 changed files with 21 additions and 348 deletions.
diff --git a/subworkflows/nf-neuro/preproc_t1/main.nf b/subworkflows/nf-neuro/preproc_t1/main.nf
@@ -41,9 +41,7 @@ workflow PREPROC_T1 {
 
         // ** Brain extraction ** //
         if ( params.run_synthbet) {
-        BETCROP_ANTSBET ( ch_bet )
             ch_bet = IMAGE_RESAMPLE.out.image.join(ch_weights)
-        ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
             BETCROP_SYNTHBET ( ch_bet )
             ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())
 
@@ -65,12 +63,12 @@ workflow PREPROC_T1 {
         }
 
         // ** crop image ** //
-        ch_crop = image_bet.t1.map{it + [[]]}
+        ch_crop = image_bet.map{it + [[]]}
         BETCROP_CROPVOLUME_T1 ( ch_crop )
         ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())
 
         // ** crop mask ** //
-        ch_crop_mask = mask_bet.mask.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
+        ch_crop_mask = mask_bet.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
         BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
         ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())
 

diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config
@@ -0,0 +1,19 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "IMAGE_RESAMPLE" {
+        ext.voxel_size = 1
+        ext.interp = "lin"
+    }
+    withName: "BETCROP_CROPVOLUME_T1" {
+        ext.output_bbox = true
+        ext.first_suffix = "t1"
+    }
+    withName: "BETCROP_SYNTHBET" {
+        memory = 8.GB
+        ext.nocsf = true
+    }
+}
+
+params {
+    run_synthbet = true
+}