New density map module

modules/nf-neuro/tractogram/densitymap/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: tractogram_densitymap

modules/nf-neuro/tractogram/densitymap/main.nf

@@ -0,0 +1,46 @@
+process TRACTOGRAM_DENSITYMAP {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(tractogram)
+
+    output:
+    tuple val(meta), path("*__*.nii.gz"), emit: density_map
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def binary = task.ext.is_binary ? "--binary" : ""
+    """
+    bname=\$(basename ${tractogram} .trk)
+    scil_tractogram_compute_density_map.py $tractogram ${prefix}__\${bname}.nii.gz ${binary}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list --disable-pip-version-check --no-python-version-warning | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    scil_tractogram_compute_density_map.py -h
+
+    touch ${prefix}_AF_L.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list --disable-pip-version-check --no-python-version-warning | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/nf-neuro/tractogram/densitymap/meta.yml

@@ -0,0 +1,45 @@
+---
+name: "tractogram_densitymap"
+description: Compute density maps from tractograms
+keywords:
+  - Diffusion MRI
+  - Tractogram
+  - Density Map
+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:'test', single_end:false ]`
+
+  - tractogram:
+      type: file
+      description: Tractogram file for density map computation
+      pattern: "*.trk"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - density_map:
+      type: file
+      description: Computed density map
+      pattern: "*.nii.gz"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@GuillaumeTh"
+maintainers:
+  - "@GuillaumeTh"

modules/nf-neuro/tractogram/densitymap/tests/main.nf.test

@@ -0,0 +1,75 @@
+nextflow_process {
+
+    name "Test Process TRACTOGRAM_DENSITYMAP"
+    script "../main.nf"
+    process "TRACTOGRAM_DENSITYMAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tractogram"
+    tag "tractogram/densitymap"
+
+    tag "subworkflows"
+    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( [ "bundles.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("densitymap - map") {
+
+        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")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("densitymap - mask") {
+
+        config "./nextflow_mask.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")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-neuro/tractogram/densitymap/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "densitymap - map": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_all_1mm.nii.gz:md5,a9cc8ba016a680ec8cbac940c45e5464"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7a2b58d5ff9231cb698c8ca1a279171f"
+                ],
+                "density_map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_all_1mm.nii.gz:md5,a9cc8ba016a680ec8cbac940c45e5464"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a2b58d5ff9231cb698c8ca1a279171f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T13:26:09.344942322"
+    },
+    "densitymap - mask": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_all_1mm.nii.gz:md5,5c682d295c593e132295e21e753a6f4f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7a2b58d5ff9231cb698c8ca1a279171f"
+                ],
+                "density_map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bundle_all_1mm.nii.gz:md5,5c682d295c593e132295e21e753a6f4f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7a2b58d5ff9231cb698c8ca1a279171f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T13:26:15.496099088"
+    }
+}

modules/nf-neuro/tractogram/densitymap/tests/nextflow_mask.config

@@ -0,0 +1,6 @@
+process {
+    withName: "TRACTOGRAM_DENSITYMAP" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.is_binary = true
+    }
+}

modules/nf-neuro/tractogram/densitymap/tests/tags.yml

@@ -0,0 +1,2 @@
+tractogram/densitymap:
+  - "modules/nf-neuro/tractogram/densitymap/**"