[WIP] add t1 option in fslbetcrop module

.github/workflows/test.yml

@@ -78,7 +78,7 @@ jobs:
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"
-          token: ""
+          token: "${{ secrets.GITHUB_TOKEN }}"
 
   nf-core-lint:
     runs-on: scilus-nf-scil-runners

modules/nf-scil/betcrop/fslbetcrop/main.nf

@@ -8,13 +8,13 @@ process BETCROP_FSLBETCROP {
         'scilus/scilus:1.6.0' }"
 
     input:
-        tuple val(meta), path(dwi), path(bval), path(bvec)
+        tuple val(meta), path(image), path(bval), path(bvec)
 
     output:
-        tuple val(meta), path("*dwi_bet_cropped.nii.gz")            , emit: dwi
-        tuple val(meta), path("*dwi_bet_cropped_mask.nii.gz")       , emit: mask
-        tuple val(meta), path("*dwi_boundingBox.pkl")               , emit: bbox
-        path "versions.yml"                                         , emit: versions
+        tuple val(meta), path("*_bet_cropped.nii.gz")            , emit: image
+        tuple val(meta), path("*_bet_cropped_mask.nii.gz")       , emit: mask
+        tuple val(meta), path("*_boundingBox.pkl")               , emit: bbox
+        path "versions.yml"                                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,31 +23,53 @@ process BETCROP_FSLBETCROP {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     def b0_thr = task.ext.b0_thr ? "--b0_thr " + task.ext.b0_thr : ""
-    def bet_dwi_f = task.ext.bet_dwi_f ? "-f " + task.ext.bet_dwi_f : ""
+    def bet_f = task.ext.bet_f ? "-f " + task.ext.bet_f : ""
 
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
-    scil_extract_b0.py $dwi $bval $bvec ${prefix}__b0.nii.gz --mean \
-        $b0_thr --force_b0_threshold
-    bet ${prefix}__b0.nii.gz ${prefix}__b0_bet.nii.gz -m -R $bet_dwi_f
-    scil_image_math.py convert ${prefix}__b0_bet_mask.nii.gz ${prefix}__b0_bet_mask.nii.gz --data_type uint8 -f
-    mrcalc $dwi ${prefix}__b0_bet_mask.nii.gz -mult ${prefix}__dwi_bet.nii.gz -quiet -nthreads 1
+    if [[ -v $bval && -v $bvec ]]
+    then
+        scil_extract_b0.py $image $bval $bvec ${prefix}__b0.nii.gz --mean \
+            $b0_thr --force_b0_threshold
 
-    scil_crop_volume.py $dwi ${prefix}__dwi_bet_cropped.nii.gz -f \
-        --output_bbox ${prefix}__dwi_boundingBox.pkl -f
-    scil_crop_volume.py ${prefix}__b0_bet_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz -f\
-        --input_bbox ${prefix}__dwi_boundingBox.pkl -f
-    scil_image_math.py convert ${prefix}__dwi_bet_cropped_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz \
-        --data_type uint8 -f
+        bet ${prefix}__b0.nii.gz ${prefix}__b0_bet.nii.gz -m -R $bet_f
+        scil_image_math.py convert ${prefix}__b0_bet_mask.nii.gz ${prefix}__b0_bet_mask.nii.gz --data_type uint8 -f
+        mrcalc $image ${prefix}__b0_bet_mask.nii.gz -mult ${prefix}__dwi_bet.nii.gz -quiet -nthreads 1
+
+        if ( "$task.ext.crop" = true );
+        then
+            scil_crop_volume.py $image ${prefix}__dwi_bet_cropped.nii.gz -f \
+                --output_bbox ${prefix}__dwi_boundingBox.pkl -f
+            scil_crop_volume.py ${prefix}__b0_bet_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz -f\
+                --input_bbox ${prefix}__dwi_boundingBox.pkl -f
+            scil_image_math.py convert ${prefix}__dwi_bet_cropped_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz \
+                --data_type uint8 -f
+        fi
+
+    else
+        bet $image ${prefix}__t1_bet.nii.gz -m -R $bet_f
+        scil_image_math.py convert ${prefix}__t1_bet_mask.nii.gz ${prefix}__t1_bet_mask.nii.gz --data_type uint8 -f 
+
+        if ( "$task.ext.crop" = true );
+        then
+            scil_crop_volume.py $image ${prefix}__t1_bet_cropped.nii.gz -f \
+                --output_bbox ${prefix}__t1_boundingBox.pkl -f
+            scil_crop_volume.py ${prefix}__t1_bet_mask.nii.gz ${prefix}__t1_bet_cropped_mask.nii.gz -f\
+                --input_bbox ${prefix}__dwi_boundingBox.pkl -f
+            scil_image_math.py convert ${prefix}__t1_bet_cropped_mask.nii.gz ${prefix}__t1_bet_cropped_mask.nii.gz \
+                --data_type uint8 -f
+        fi
+    fi     
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: 1.6.0
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+
     END_VERSIONS
     """
 
@@ -64,6 +86,7 @@ process BETCROP_FSLBETCROP {
 
     touch ${prefix}__dwi_bet_cropped.nii.gz
     touch ${prefix}__dwi_bet_cropped_mask.nii.gz
+    touch ${prefix}__dwi_boundingBox.pkl
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-scil/betcrop/fslbetcrop/meta.yml

@@ -4,6 +4,7 @@ name: "betcrop_fslbetcrop"
 description: Perform Brain extraction using FSL BET followed by cropping empty planes around the data.
 keywords:
   - DWI
+  - T1
   - BET
   - Crop
 tools:
@@ -24,9 +25,9 @@ input:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - dwi:
+  - image:
       type: file
-      description: Nifti DWI volume to perform BET + crop.
+      description: Nifti image volume to perform BET + crop.
       pattern: "*.{nii,nii.gz}"
 
   - bval:
@@ -46,19 +47,19 @@ output:
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
 
-  - dwi:
+  - image:
       type: file
-      description: Nifti DWI volume brain-extracted and cropped.
-      pattern: "*dwi_bet_cropped.{nii,nii.gz}"
+      description: Nifti volume brain-extracted and cropped.
+      pattern: "*_bet_cropped.{nii,nii.gz}"
 
   - mask:
       type: file
-      description: DWI mask brain-extracted and cropped.
-      pattern: "*dwi_bet_cropped_mask.{nii,nii.gz}"
+      description: mask brain-extracted and cropped.
+      pattern: "*_bet_cropped_mask.{nii,nii.gz}"
 
   - bbox:
       type: file
-      description: DWI BoundingBox used for cropping.
+      description: BoundingBox used for cropping.
       pattern: "*dwi_boundingBox.pkl"
 
   - versions:

tests/modules/nf-scil/betcrop/fslbetcrop/main.nf

@@ -3,9 +3,10 @@
 nextflow.enable.dsl = 2
 
 include { BETCROP_FSLBETCROP } from '../../../../../modules/nf-scil/betcrop/fslbetcrop/main.nf'
+include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main'
 
-workflow test_betcrop_fslbetcrop {
-
+workflow test_betcrop_fslbetcrop_dwi {
+    
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['betcrop']['fslbetcrop']['dwi'], checkIfExists: true),
@@ -15,3 +16,19 @@ workflow test_betcrop_fslbetcrop {
 
     BETCROP_FSLBETCROP ( input )
 }
+
+workflow test_betcrop_fslbetcrop_t1 {
+
+    input_fetch = Channel.from( [ "others.zip" ] )
+
+    LOAD_TEST_DATA ( input_fetch, "test.test_betcrop_fslbetcrop_t1" )
+
+    input = LOAD_TEST_DATA.out.test_data_directory
+    .map{ test_data_directory -> [
+        [ id:'test', single_end:false ], // meta map
+        file("${test_data_directory}/t1.nii.gz")
+
+    ]}
+
+    BETCROP_FSLBETCROP ( input )
+}

tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config

@@ -3,7 +3,13 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: "BETCROP_FSLBETCROP" {
-        ext.bet_dwi_f = 0.16
+        ext.bet_f = 0.16
         ext.b0_thr = 10
+        ext.crop = false
+    }
+
+        withName: "workflow test_betcrop_fslbetcrop_t1:BETCROP_FSLBETCROP" {
+        ext.bet_f = 0.5
+        ext.crop = true
     }
 }