[WIP] Module: bundle/bundleparc

modules/nf-neuro/bundle/bundleparc/environment.yml

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+channels: []
+dependencies: []
+name: bundle_bundleparc

modules/nf-neuro/bundle/bundleparc/main.nf

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+process BUNDLE_BUNDLEPARC {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "scilus/scilus:2.2.0"
+
+    input:
+        tuple val(meta), path(fodf), path(checkpoint)
+
+    output:
+        tuple val(meta), path("*.nii.gz"),  emit: labels
+        path "versions.yml",                emit: versions
+        path "*__bundleparc_config.json",   emit: config
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def nb_pts = task.ext.nb_pts ?: 10
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+
+    stride="\$( mrinfo -stride $fodf )"
+    if [[ "\$stride" == "-1 2 3 4" ]]; then
+        scil_fodf_bundleparc $fodf \
+            --out_prefix ${prefix}__ \
+            --nb_pts ${nb_pts} \
+            --out_folder tmp \
+            --checkpoint ${checkpoint} \
+            --keep_biggest
+        mv tmp/* .
+        rm -r tmp
+    else
+        echo "Invalid stride ("\$stride"), must be -1 2 3 4"
+        exit 1
+    fi
+    cat <<-BUNDLEPARC_INFO > ${prefix}__bundleparc_config.json
+    {"nb_pts": "${task.ext.nb_pts}"}
+    BUNDLEPARC_INFO
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    scil_fodf_bundleparc -h
+
+    touch ${prefix}__AF_left.nii.gz
+    ${prefix}__bundleparc_config.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/nf-neuro/bundle/bundleparc/meta.yml

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+name: "bundle_bundleparc"
+description: |
+  BundleParc performs bundle segmentation and parcellation directly from fODFs
+  for a specified number of points/segments/labels.
+
+  Bundle definitions follow TractSeg's, without the whole corpus callosum.
+  However it is still represented in 7 subparts which should be coherent
+  between their parcellations.
+
+  If you use this subworkflow, please cite:
+  [1] Théberge, Antoine, Descoteaux, Maxime, Jodoin, P-M.
+      "BundleParc: off-the-shelf bundle parcellation without tractography."
+      Submitted to Medical Image Analysis (2025).
+keywords:
+  - BundleParc
+  - Bundle
+  - Parcellation
+tools:
+  - "bundleparc":
+      description: |
+        BundleParc: off-the-shelf bundle parcellation without tractography.
+      homepage: "https://github.com/scil-vital/BundleParc"
+      tool_dev_url: "https://github.com/scil-vital/BundleParc-flow"
+      identifier: ""
+  - scilpy:
+      description: The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI
+        processing toolbox.
+      homepage: https://github.com/scilus/scilpy.git
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fodf:
+        type: file
+        description: |
+          The fODF image in the descoteaux_legacy and order 8 format (very
+          important).
+        pattern: "*.{nii,nii.gz}"
+        ontologies: []
+    - checkpoint:
+        type: file
+        description: |
+          Since BundleParc relies on deep learning, the checkpoint represents
+          the learned weights of BundleParc's underlying model, which is
+          essential for its operation. The checkpoint file should be
+          downloaded automatically when using the subworkflow, otherwise it
+          can be found at:
+          https://zenodo.org/records/15579498/files/123_4_5_bundleparc.ckpt
+        pattern: "123_4_5_bundleparc.ckpt"
+        ontologies: []
+args:
+  - nb_points:
+      type: int
+      description: |
+        Number of regions/points to parcellate the bundles into.
+      default: 10
+output:
+  labels:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.nii.gz":
+          type: file
+          description: |
+            The output parcellated bundles.
+          pattern: "*.{nii.gz}"
+          ontologies: []
+  config:
+    - "*__bundleparc_config.json":
+        type: file
+        description: Parameters used to obtain the output parcellation files.
+        pattern: "*__bundleparc_config.json"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464" # JSON
+  versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@AntoineTheb"
+maintainers:
+  - "@levje"

modules/nf-neuro/bundle/bundleparc/tests/main.nf.test

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+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test bundle/bundleparc
+nextflow_process {
+
+    name "Test Process BUNDLE_BUNDLEPARC"
+    script "../main.nf"
+    process "BUNDLE_BUNDLEPARC"
+
+    tag "modules"
+    tag "modules_nfneuro"
+    tag "bundle"
+    tag "bundle/bundleparc"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}

subworkflows/nf-neuro/bundleparc/main.nf

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+include { BUNDLE_BUNDLEPARC } from '../../../modules/nf-neuro/bundle/bundleparc/main.nf'
+
+def compute_file_hash(file_path) {
+    def file = new File(file_path)
+    if (!file.exists()) {
+        error "File not found: $file_path"
+    }
+
+    def digest = java.security.MessageDigest.getInstance("MD5")
+    def fileBytes = java.nio.file.Files.readAllBytes(java.nio.file.Paths.get(file_path))
+    def hashBytes = digest.digest(fileBytes)
+    return hashBytes.collect { String.format("%02x", it) }.join('')
+}
+
+def fetch_bundleparc_checkpoint(dest) {
+    def checkpoint_url = "https://zenodo.org/records/15579498/files/123_4_5_bundleparc.ckpt"
+    def checkpoint_md5 = ""
+
+    if (file("$workflow.workDir/weights/123_4_5_bundleparc.ckpt").exists()) {
+        def existing_md5 = compute_file_hash("$workflow.workDir/weights/123_4_5_bundleparc.ckpt")
+        if (existing_md5 == checkpoint_md5) {
+            println "BundleParc checkpoint already exists and is valid."
+            return "$workflow.workDir/weights/123_4_5_bundleparc.ckpt"
+        } else {
+            println "Existing BundleParc checkpoint is invalid. Re-downloading..."
+            new File("$workflow.workDir/weights/123_4_5_bundleparc.ckpt").delete()
+        }
+    }
+
+    def path = java.nio.file.Paths.get("$dest/weights/")
+    if (!java.nio.file.Files.exists(path)) {
+        java.nio.file.Files.createDirectories(path)
+    }
+
+    println("Downloading BundleParc checkpoint from $checkpoint_url...")
+    def weights = new File("$dest/weights/123_4_5_bundleparc.ckpt").withOutputStream { out ->
+        new URL(checkpoint_url).withInputStream { from -> out << from; }
+    }
+    println("Download completed.")
+
+    return weights
+}
+
+workflow BUNDLEPARC {
+
+    take:
+        ch_fodf // channel: [ val(meta), [ fodf ] ]
+
+    main:
+        ch_versions = Channel.empty()
+        ch_multiqc_files = Channel.empty()
+
+        if ( params.checkpoint ) {
+            weights = Channel.fromPath("$params.checkpoint", checkIfExists: true, relative: true)
+        }
+        else {
+            if ( !file("$workflow.workDir/weights/123_4_5_bundleparc.ckpt").exists() ) {
+                fetch_bundleparc_checkpoint("${workflow.workDir}/")
+            }
+            weights = Channel.fromPath("$workflow.workDir/weights/123_4_5_bundleparc.ckpt", checkIfExists: true)
+        }
+
+        ch_fodf =  ch_fodf.combine(weights)
+
+        BUNDLE_BUNDLEPARC(ch_fodf)
+        ch_versions = ch_versions.mix(BUNDLE_BUNDLEPARC.out.versions)
+
+    emit:
+        bundles     = BUNDLE_BUNDLEPARC.out.labels // channel: [ val(meta), [ bundles ] ]
+        mqc         = ch_multiqc_files             // channel: [ multiqc files ]
+        versions    = ch_versions                  // channel: [ versions.yml ]
+}

subworkflows/nf-neuro/bundleparc/meta.yml

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+name: "bundleparc"
+description: |
+  BundleParc performs bundle segmentation and parcellation directly from fODFs
+  for a specified number of points/segments/labels.
+
+  Bundle definitions follow TractSeg's, without the whole corpus callosum.
+  However it is still represented in 7 subparts which should be coherent
+  between their parcellations.
+
+  If you use this subworkflow, please cite:
+  [1] Théberge, Antoine, Descoteaux, Maxime, Jodoin, P-M.
+      "BundleParc: off-the-shelf bundle parcellation without tractography."
+      Submitted to Medical Image Analysis (2025).
+keywords:
+  - BundleParc
+  - Bundle
+  - Parcellation
+components:
+  - bundle/bundleparc
+input:
+  - ch_fodf:
+      type: file
+      description: |
+        The input channel containing the fODF image in descoteaux07_legacy
+        format (very important).
+      pattern: "*.{nii,nii.gz}"
+output:
+  - bundles:
+      type: file
+      description: |
+        Channel containing all the parcellated bundle files.
+        Structure: [ val(meta), path(bundles) ]
+      pattern: "*.nii.gz"
+  - mqc:
+      type: file
+      description: |
+        Channel containing mosaics of a subset of bundles for QC purposes.
+        Structure: [ val(meta), path(mqc) ]
+      pattern: "*mqc.png"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@AntoineTheb"
+maintainers:
+  - "@levje"