[Subworkflow][WIP] Tractoflow

.github/workflows/nf-test_module.yml

@@ -115,6 +115,7 @@ jobs:
             ${{ inputs.paths }}
 
       - uses: pcolby/tap-summary@v1
+        if: always()
         with:
           path: >-
             test.tap

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

@@ -1,14 +1,14 @@
 
 process BETCROP_ANTSBET {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
         'scilus/scilus:2.0.0' }"
 
     input:
-    tuple val(meta), path(t1), path(template), path(tissues_probabilities)
+    tuple val(meta), path(t1), path(template), path(tissues_probabilities), path(mask), path(initial_affine)
 
     output:
     tuple val(meta), path("*t1_bet.nii.gz")     , emit: t1
@@ -19,18 +19,24 @@ process BETCROP_ANTSBET {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = []
+    if (mask) args += ["-f $mask"]
+    if (initial_affine) args += ["-r $initial_affine"]
 
     """
-    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
     export ANTS_RANDOM_SEED=1234
 
-    antsBrainExtraction.sh -d 3 -a $t1 -e $template -o bet/ -m $tissues_probabilities -u 0
-    scil_volume_math.py convert bet/BrainExtractionMask.nii.gz ${prefix}__t1_bet_mask.nii.gz --data_type uint8
-    mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads 1
+    antsBrainExtraction.sh -d 3 -a $t1 -o bet/ -u 0 \
+        -e $template -m $tissues_probabilities ${args.join(' ')}
+
+    scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \
+        ${prefix}__t1_bet_mask.nii.gz --data_type uint8
+
+    mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads $task.cpus
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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

@@ -35,9 +35,25 @@ input:
 
   - tissues_probabilities:
       type: file
-      description: Brain probability mask, with intensity range 1 (definitely brain) to 0 (definitely background).
+      description: |
+        Brain probability mask (in template space), with intensity
+        range 1 (definitely brain) to 0 (definitely background).
       pattern: "*.{nii,nii.gz}"
 
+  - mask:
+      type: file
+      description: |
+        Brain mask (in template space) used to restrict metric
+        computation when performing registration.
+      pattern: "*.{nii,nii.gz}"
+
+  - initial_affine:
+      type: file
+      description: |
+        Affine transform from T1w space to DWI space, used as
+        initialization for registration algorithms
+      pattern: "*.{mat/txt}"
+
 output:
   - meta:
       type: map

modules/nf-scil/betcrop/antsbet/tests/main.nf.test

@@ -20,7 +20,7 @@ nextflow_process {
                 script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
                 process {
                     """
-                    input[0] = Channel.from( [ "antsbet.zip" ] )
+                    input[0] = Channel.from( [ "T1w.zip", "transform.zip", "antsbet.zip" ] )
                     input[1] = "test.load-test-data"
                     """
                 }
@@ -30,14 +30,41 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = LOAD_DATA.out.test_data_directory.map{
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        t1: it.simpleName == "T1w"
+                        transform: it.simpleName == "transform"
+                        template: it.simpleName == "antsbet"
+                    }
+                ch_t1 = ch_split_test_data.t1.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ], // meta map
-                        file("\${test_data_directory}/t1_unaligned.nii.gz"),
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_template = ch_split_test_data.template.map{
+                    test_data_directory -> [
+                        [ id: 'test' ],
                         file("\${test_data_directory}/t1_template.nii.gz"),
                         file("\${test_data_directory}/t1_brain_probability_map.nii.gz")
                     ]
                 }
+                ch_mask = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template_mask.nii.gz")
+                    ]
+                }
+                ch_transform = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template.mat")
+                    ]
+                }
+                input[0] = ch_t1
+                    .join(ch_template)
+                    .join(ch_mask)
+                    .join(ch_transform)
                 """
             }
         }

modules/nf-scil/betcrop/antsbet/tests/main.nf.test.snap

@@ -5,19 +5,17 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__t1_bet.nii.gz:md5,31ccfe501376952248b4d933645f1304"
+                        "test__t1_bet.nii.gz:md5,7e123ce5b3485dcf59189626b372a998"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__t1_bet_mask.nii.gz:md5,0874069d069f06bfc40d7f6be2347259"
+                        "test__t1_bet_mask.nii.gz:md5,d19f11a798ced79cc8d1e0cb5fc6294b"
                     ]
                 ],
                 "2": [
@@ -26,19 +24,17 @@
                 "mask": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__t1_bet_mask.nii.gz:md5,0874069d069f06bfc40d7f6be2347259"
+                        "test__t1_bet_mask.nii.gz:md5,d19f11a798ced79cc8d1e0cb5fc6294b"
                     ]
                 ],
                 "t1": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__t1_bet.nii.gz:md5,31ccfe501376952248b4d933645f1304"
+                        "test__t1_bet.nii.gz:md5,7e123ce5b3485dcf59189626b372a998"
                     ]
                 ],
                 "versions": [
@@ -47,9 +43,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-04-23T16:07:14.789765"
+        "timestamp": "2024-08-01T04:39:54.352166"
     }
 }

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

@@ -2,4 +2,5 @@ process {
     withName: "BETCROP_ANTSBET" {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     }
+    cpus = 1
 }

modules/nf-scil/denoising/mppca/main.nf

@@ -1,14 +1,14 @@
 
 process DENOISING_MPPCA {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
         'scilus/scilus:2.0.0' }"
 
     input:
-    tuple val(meta), path(dwi)
+    tuple val(meta), path(dwi), path(mask)
 
     output:
     tuple val(meta), path("*_dwi_denoised.nii.gz")  , emit: image
@@ -20,13 +20,16 @@ process DENOISING_MPPCA {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extent = task.ext.extent ? "-extent " + task.ext.extent : ""
+    def args = ["-nthreads ${task.cpus - 1}"]
+    if (mask) args += ["-mask $mask"]
 
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
+    export MRTRIX_RNG_SEED=112524
 
-    dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent -nthreads 1
+    dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")}
     fslmaths ${prefix}_dwi_denoised.nii.gz -thr 0 ${prefix}_dwi_denoised.nii.gz
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-scil/denoising/mppca/meta.yml

@@ -28,6 +28,11 @@ input:
       description: Nifti dwi file to denoise
       pattern: "*.{nii,nii.gz}"
 
+  - mask:
+      type: file
+      description: Nifti mask file for the dwi, optional
+      pattern: "*.{nii,nii.gz}"
+
 output:
   - meta:
       type: map

modules/nf-scil/denoising/mppca/tests/main.nf.test

@@ -20,7 +20,7 @@ nextflow_process {
                 script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
                 process {
                     """
-                    input[0] = Channel.from( [ "heavy.zip" ] )
+                    input[0] = Channel.from( [ "raw_DWIss300-dir8.zip", "raw_segmentation.zip" ] )
                     input[1] = "test.load-test-data"
                     """
                 }
@@ -30,12 +30,25 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = LOAD_DATA.out.test_data_directory.map{
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        dwi: it.simpleName == "raw_DWIss300-dir8"
+                        segmentation: it.simpleName == "raw_segmentation"
+                    }
+                ch_dwi = ch_split_test_data.dwi.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ], // meta map
-                        file("\${test_data_directory}/dwi/dwi.nii.gz")
+                        [ id:'test' ],
+                        file("\${test_data_directory}/dwi.nii.gz")
                     ]
                 }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/slices/axial.nii.gz")
+                    ]
+                }
+                input[0] = ch_dwi
+                    .join(ch_mask)
                 """
             }
         }

modules/nf-scil/denoising/mppca/tests/main.nf.test.snap

@@ -5,10 +5,9 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596"
+                        "test_dwi_denoised.nii.gz:md5,7ede52f321a38e6d171c01504b2e5b4c"
                     ]
                 ],
                 "1": [
@@ -17,10 +16,9 @@
                 "image": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596"
+                        "test_dwi_denoised.nii.gz:md5,7ede52f321a38e6d171c01504b2e5b4c"
                     ]
                 ],
                 "versions": [
@@ -29,9 +27,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-04-25T11:07:06.152814"
+        "timestamp": "2024-07-29T03:06:13.465555"
     }
 }

modules/nf-scil/denoising/mppca/tests/nextflow.config

@@ -3,4 +3,5 @@ process {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
         ext.extent = 3
     }
+    cpus = 1
 }

modules/nf-scil/denoising/nlmeans/main.nf

@@ -1,7 +1,7 @@
 
 process DENOISING_NLMEANS {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_medium'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
@@ -19,15 +19,16 @@ process DENOISING_NLMEANS {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def args = []
+    def ncoils = task.ext.number_of_coils ?: 1
+    def args = ["--processes $task.cpus"]
     if (mask) args += ["--mask $mask"]
 
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
 
-    scil_denoising_nlmeans.py $image ${prefix}_denoised.nii.gz 1 ${args.join(" ")}
+    scil_denoising_nlmeans.py $image ${prefix}_denoised.nii.gz $ncoils ${args.join(" ")}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":