[WIP] add module decompose connectivity

modules/nf-neuro/connectivity/decompose/environment.yml

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+channels: []
+dependencies: []
+name: connectivity_decompose

modules/nf-neuro/connectivity/decompose/main.nf

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+process CONNECTIVITY_DECOMPOSE {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(trk), path(labels)
+
+    output:
+    tuple val(meta), path("*__decomposed.h5")       , emit: hdf5
+    tuple val(meta), path("*__labels_list.txt")     , emit: labels_list
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def no_pruning = task.ext.no_pruning ? "--no_pruning" : ""
+    def no_remove_loops = task.ext.no_remove_loops ? "--no_remove_loops" : ""
+    def no_remove_outliers = task.ext.no_remove_outliers ? "--no_remove_outliers" : ""
+    def no_remove_curv = task.ext.no_remove_curv ? "--no_remove_curv" : ""
+
+    def min_len = task.ext.min_len ? "--min_len " + task.ext.min_len : ""
+    def max_len = task.ext.max_len ? "--max_len " + task.ext.max_len : ""
+    def outlier_threshold = task.ext.outlier_threshold ? "--outlier_threshold " + task.ext.outlier_threshold : ""
+    def max_angle = task.ext.max_angle ? "--loop_max_angle " + task.ext.max_angle : ""
+    def max_curv = task.ext.max_curv ? "--curv_qb_distance " + task.ext.max_curv : ""
+
+    """
+
+    scil_decompose_connectivity.py $trk  $labels \
+        "${prefix}__decomposed.h5" --processes $task.cpus \
+        --out_labels_list "${prefix}__labels_list.txt" \
+        $no_pruning $no_remove_loops $no_remove_outliers \
+        $no_remove_curv $min_len $max_len $outlier_threshold \
+        $max_angle $max_curv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}__decomposed.h5
+    touch ${prefix}__labels_list.txt
+
+    scil_decompose_connectivity.py -h
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/nf-neuro/connectivity/decompose/meta.yml

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+---
+name: "connectivity_decompose"
+description: Divide a tractogram into its various connections using a brain parcellation(labels).
+  The hdf5 output format allows to store other information required for connectivity, such as the associated labels.
+keywords:
+  - nifti
+  - connectivity
+  - decompose
+  - scilpy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - trk:
+      type: file
+      description: Tractogram to decompose.
+      pattern: "*.{trk, tck, vtk, fib, dpy}"
+
+  - labels:
+      type: file
+      description: brain parcellation. Labels must have 0 as background. Volumes must have isotropic voxels.
+      pattern: "*.nii.gz"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - hdf5:
+      type: file
+      description: |
+        Output hdf5 file where each bundles is a group with key'LABEL1_LABEL2'.
+        The array_sequence format cannot be stored directly in a hdf5, so each
+        group is composed of 'data', 'offsets' and 'lengths' from the array
+        sequence. The 'data' is stored in VOX/CORNER for simplicity and efficiency.
+      pattern: "*__decomposed.h5"
+
+  - labels_list:
+      type: file
+      description: Save the labels list as text file.
+      pattern: "*__labels_list.txt"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"
+maintainers:
+  - "@ThoumyreStanislas"

modules/nf-neuro/connectivity/decompose/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process CONNECTIVITY_DECOMPOSE"
+    script "../main.nf"
+    process "CONNECTIVITY_DECOMPOSE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "connectivity"
+    tag "connectivity/decompose"
+
+    tag "subworkflows/load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "connectivity.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("connectivity - decompose - without option") {
+        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}/bundle_all_1mm.trk", checkIfExists: true),
+                        file("\${test_data_directory}/endpoints_atlas.nii.gz", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+        test("connectivity - decompose - with all option") {
+        config "./nextflow.config"
+        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}/bundle_all_1mm.trk", checkIfExists: true),
+                        file("\${test_data_directory}/endpoints_atlas.nii.gz", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+        test("connectivity - visualisation - stub-run") {
+        options "-stub-run"
+        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}/bundle_all_1mm.trk", checkIfExists: true),
+                        file("\${test_data_directory}/endpoints_atlas.nii.gz", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+}

modules/nf-neuro/connectivity/decompose/tests/main.nf.test.snap

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+{
+    "connectivity - decompose - without option": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__decomposed.h5:md5,90ff9ae7ceb1371349231f85b616874e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__labels_list.txt:md5,3b0332e02daabf31651a5a0d81ba830a"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,ca6d20bf86c1e32c1bccea5813810f02"
+                ],
+                "hdf5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__decomposed.h5:md5,90ff9ae7ceb1371349231f85b616874e"
+                    ]
+                ],
+                "labels_list": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__labels_list.txt:md5,3b0332e02daabf31651a5a0d81ba830a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ca6d20bf86c1e32c1bccea5813810f02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T12:03:16.31875384"
+    },
+    "connectivity - visualisation - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,ca6d20bf86c1e32c1bccea5813810f02"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T12:03:27.09566413"
+    },
+    "connectivity - decompose - with all option": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__decomposed.h5:md5,5660bb84f333b6586ed247c6b95f6a98"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__labels_list.txt:md5,3b0332e02daabf31651a5a0d81ba830a"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,ca6d20bf86c1e32c1bccea5813810f02"
+                ],
+                "hdf5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__decomposed.h5:md5,5660bb84f333b6586ed247c6b95f6a98"
+                    ]
+                ],
+                "labels_list": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__labels_list.txt:md5,3b0332e02daabf31651a5a0d81ba830a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ca6d20bf86c1e32c1bccea5813810f02"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T12:03:21.738887954"
+    }
+}

modules/nf-neuro/connectivity/decompose/tests/nextflow.config

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+process {
+    withName: "CONNECTIVITY_DECOMPOSE" {
+        ext.no_pruning = true
+        ext.no_remove_loops = true
+        ext.no_remove_outliers = true
+        ext.no_remove_curv = true
+        ext.min_len = 20.0
+        ext.max_len = 200.0
+        ext.outlier_threshold = 0.6
+        ext.max_angle = 330.0
+        ext.max_curv = 10.0
+        }
+    }

modules/nf-neuro/connectivity/decompose/tests/tags.yml

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+connectivity/decompose:
+  - "modules/nf-neuro/connectivity/decompose/**"