[WIP][MODULE] Add module vascular

modules/nf-neuro/vascular/eicab/environment.yml

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+channels: []
+dependencies: []
+name: vascular_eicab
+

modules/nf-neuro/vascular/eicab/main.nf

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+
+process VASCULAR_EICAB {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ 'felixdumais1/eicab:v1.0.1' }"
+    containerOptions {
+        (workflow.containerEngine == 'docker') ? '--entrypoint ""' : ''
+    }
+
+    input:
+        tuple val(meta), path(in_tof)
+
+    output:
+        tuple val(meta), path("*_eicab")                  , emit: eicabdirectory
+        tuple val(meta), path("*_eicab/*_eICAB_CW.nii.gz"), emit: eicabcw
+        path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def out_folder = task.ext.out_folder ?: "${prefix}_eicab"
+    def resolution = task.ext.resolution ?: "0.625"
+    """
+    /vessel_segmentation_snaillab/eICAB.sh -t $in_tof \
+                                           -o $out_folder \
+                                           -r $resolution
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vessel-segmentation: \$(pip list | grep vessel-segmentation | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}_eicab/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vessel-segmentation: \$(pip list | grep vessel-segmentation | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/nf-neuro/vascular/eicab/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "vascular_eicab"
+description: |
+  eICAB automatically segments and labels the Internal Carotid Arteries (ICA), Basilar Artery (BA), Anterior Communicating
+  Artery (AComm), Anterior Cerebral Arteries (ACA), Middle Cerebral Arteries (MCA), Posterior Communicating Arteries (
+  PComm), Posterior Cerebral Arteries (PCA), Superior Cerebellar Arteries (SCA) and Anterior Choroidal Arteries (AChA).
+keywords:
+  - angiography
+  - segmentation
+  - labelling
+  - vascular
+tools:
+  - "vascular":
+      homepage: "https://gitlab.com/FelixDumais/vessel_segmentation_snaillab/"
+      description: "Automated segmentation and labeling of the main intracranial arteries on MR angiography images"
+      tool_dev_url: "https://gitlab.com/FelixDumais/vessel_segmentation_snaillab/"
+      doi: "10.1016/j.neuroimage.2022.119425"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+      mandatory: true
+
+  - in_tof:
+      type: file
+      description: ToF MRA image
+      pattern: "*.{nii/nii.gz}"
+      mandatory: true
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - eicabdirectory:
+      type: directory
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*_eicab"
+
+  - eicabcw:
+      type: file
+      description: Segmented Circle of Willis (CW) annotated
+      pattern: "*_eicab_cw.nii.gz"
+
+authors:
+  - "@arnaudbore"
+maintainers:
+  - "@arnaudbore"
+references:
+  - "eICAB: A novel deep learning pipeline for Circle of Willis multiclass segmentation and analysis"

modules/nf-neuro/vascular/eicab/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process VASCULAR_EICAB"
+    script "../main.nf"
+    process "VASCULAR_EICAB"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vascular"
+    tag "vascular/eicab"
+
+    test("segmentation - eicab") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [ file("/workspaces/nf-neuro/data/sub-OAS30001_ses-d2430_acq-TOF_angio_resampled.nii.gz") ]
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.eicabdirectory.get(0).get(1)).name,
+                    file(process.out.eicabcw.get(0).get(1)).name,
+                    process.out.versions).match()}
+            )
+        }
+    }
+}

modules/nf-neuro/vascular/eicab/tests/main.nf.test.snap

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+{
+    "segmentation - eicab": {
+        "content": [
+            "test_eicab",
+            "sub-OAS30001_ses-d2430_acq-TOF_angio_resampled_eICAB_CW.nii.gz",
+            [
+                "versions.yml:md5,6b433c9a3e91fd2a59ac92510ccee4dd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-12T02:51:01.189807007"
+    }
+}

modules/nf-neuro/vascular/eicab/tests/tags.yml

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+vascular/eicab:
+  - "modules/nf-neuro/vascular/eicab/**"