Merge pull request #122 from anroy1/synthbet

[Module] Freesurfer BET

modules/nf-scil/betcrop/synthbet/environment.yml

@@ -0,0 +1,8 @@
+name: betcrop_synthbet
+
+channels:
+  - Docker
+  - Apptainer
+
+dependencies:
+  - "Freesurfer:synthstrip"

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

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+process BETCROP_SYNTHBET {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "freesurfer/synthstrip:latest"
+    containerOptions "--entrypoint ''"
+
+    input:
+    tuple val(meta), path(image), path(weights) /* optional, input = [] */
+
+    output:
+    tuple val(meta), path("*__bet_image.nii.gz"), emit: bet_image
+    tuple val(meta), path("*__brain_mask.nii.gz"), emit: brain_mask
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def gpu = task.ext.gpu ? "--gpu" : ""
+    def border = task.ext.border ? "-b " + task.ext.border : ""
+    def nocsf = task.ext.nocsf ? "--no-csf" : ""
+    def model = "$weights" ? "--model $weights" : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    mri_synthstrip -i $image --out ${prefix}__bet_image.nii.gz --mask ${prefix}__brain_mask.nii.gz $gpu $border $nocsf $model
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        freesurfer: 7.4
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mri_synthstrip -h
+
+    touch ${prefix}__bet_image.nii.gz
+    touch ${prefix}__brain_mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        freesurfer: 7.4
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,53 @@
+---
+name: "betcrop_synthbet"
+description: Perform brain extraction using synthstrip on image
+keywords:
+  - anatomical image
+  - BET
+  - freesurfer
+tools:
+  - "Freesurfer":
+      description: "Software package for the analysis and visualization of structural and functional neuroimaging data."
+      homepage: "https://surfer.nmr.mgh.harvard.edu/fswiki"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image volume to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - weights:
+      type: file
+      description: Alternative model weights
+      pattern: "*.pt"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - bet_image:
+      type: file
+      description: Nifti brain-extracted volume.
+      pattern: "*__bet_image.{nii,nii.gz}"
+
+  - brain_mask:
+      type: file
+      description: Brain-extracted image mask .
+      pattern: "*__brain_mask.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@anroy1"

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

@@ -0,0 +1,51 @@
+nextflow_process {
+
+    name "Test Process BETCROP_SYNTHBET"
+    script "../main.nf"
+    process "BETCROP_SYNTHBET"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "betcrop"
+    tag "betcrop/synthbet"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    test("betcrop - synthbet") {
+
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "freesurfer.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

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+{
+    "betcrop - synthbet": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bet_image.nii.gz:md5,6f5eb365a11dfc52b8c80cd7bcee7b9d"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__brain_mask.nii.gz:md5,52871114b59d09dca864cb0ea4f12832"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,f0a96d8fd7ca9d9935818dceaf91f457"
+                ],
+                "bet_image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bet_image.nii.gz:md5,6f5eb365a11dfc52b8c80cd7bcee7b9d"
+                    ]
+                ],
+                "brain_mask": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__brain_mask.nii.gz:md5,52871114b59d09dca864cb0ea4f12832"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f0a96d8fd7ca9d9935818dceaf91f457"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-06-11T14:52:54.970673"
+    }
+}

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

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+process {
+    withName: "BETCROP_SYNTHBET" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        memory = 8.GB
+        ext.nocsf = true
+    }
+}

modules/nf-scil/betcrop/synthbet/tests/tags.yml

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+betcrop/synthbet:
+  - "modules/nf-scil/betcrop/synthbet/**"