add bundle coloring module

modules/nf-scil/bundle/coloring/environment.yml

@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "bundle_coloring"
+channels:
+  - Docker
+  - Apptainer
+dependencies:
+  - "scilpy"

modules/nf-scil/bundle/coloring/main.nf

@@ -0,0 +1,53 @@
+import groovy.json.JsonOutput
+
+process BUNDLE_COLORING {
+    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(bundles)
+
+    output:
+        tuple val(meta), path("*_colored.trk")      , emit: bundles
+        path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def json_str = JsonOutput.toJson(task.ext.colors)
+    String bundles_list = bundles.join(", ").replace(',', '')
+
+    """
+    echo '$json_str' >> colors.json
+    scil_tractogram_assign_uniform_color.py --dict_colors colors.json \
+        --out_suffix "_colored" $bundles_list
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list --disable-pip-version-check --no-python-version-warning | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    for bundle in $bundles_list; do
+        bname=\$(basename \$bundle .\${ext})
+        touch \${bname}_colored.trk
+    done
+
+    scil_tractogram_assign_uniform_color.py -h
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list --disable-pip-version-check --no-python-version-warning | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

modules/nf-scil/bundle/coloring/meta.yml

@@ -0,0 +1,45 @@
+---
+name: "bundle_coloring"
+description: Assign color to bundles.
+keywords:
+  - Bundles
+  - Coloring
+  - Tractometry
+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 ]`
+
+  - bundles:
+      type: file
+      description: Flatten list of trk files containing bundles to be colored.
+      pattern: "*.trk"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - bundles:
+      type: file
+      description: Colored bundles file.
+      pattern: "*_colored.trk"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@gagnonanthony"
+maintainers:
+  - "@gagnonanthony"

modules/nf-scil/bundle/coloring/tests/main.nf.test

@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process BUNDLE_COLORING"
+    script "../main.nf"
+    process "BUNDLE_COLORING"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bundle"
+    tag "bundle/coloring"
+
+    tag "subworkflows/load_test_data"
+
+    test("bundle - coloring") {
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "bundles.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}/fibercup_atlas/subj_1/*.trk", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-scil/bundle/coloring/tests/main.nf.test.snap

@@ -0,0 +1,53 @@
+{
+    "bundle - coloring": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "bundle_0_colored.trk:md5,28654c91d0f6c5e3f3a7f101f7fd482d",
+                            "bundle_1_colored.trk:md5,3b58a00009f2bb24c4051dd88d53aeee",
+                            "bundle_2_colored.trk:md5,21d955afc36acfd8b214e562b199f929",
+                            "bundle_3_colored.trk:md5,5ce663fb79ad52f1b30fe462d5b48afe",
+                            "bundle_4_colored.trk:md5,da36a33cbaa5e38801480b51ee2943b4",
+                            "bundle_5_colored.trk:md5,0c2cd57e4372c2b71274cafc03d82490",
+                            "bundle_6_colored.trk:md5,0614ea97e6f1fa44e40cef2c2c67a4b1"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,99caf95a695ad5ae4c7e8e879af86b5a"
+                ],
+                "bundles": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "bundle_0_colored.trk:md5,28654c91d0f6c5e3f3a7f101f7fd482d",
+                            "bundle_1_colored.trk:md5,3b58a00009f2bb24c4051dd88d53aeee",
+                            "bundle_2_colored.trk:md5,21d955afc36acfd8b214e562b199f929",
+                            "bundle_3_colored.trk:md5,5ce663fb79ad52f1b30fe462d5b48afe",
+                            "bundle_4_colored.trk:md5,da36a33cbaa5e38801480b51ee2943b4",
+                            "bundle_5_colored.trk:md5,0c2cd57e4372c2b71274cafc03d82490",
+                            "bundle_6_colored.trk:md5,0614ea97e6f1fa44e40cef2c2c67a4b1"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,99caf95a695ad5ae4c7e8e879af86b5a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-10T15:52:32.023077"
+    }
+}

modules/nf-scil/bundle/coloring/tests/nextflow.config

@@ -0,0 +1,14 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "BUNDLE_COLORING" {
+        ext.colors = [
+            "bundle_0":"0xd9bd09",
+            "bundle_1":"0xcc0000",
+            "bundle_2":"0xffdf0f",
+            "bundle_3":"0x0d6cbf",
+            "bundle_4":"0xbf0099",
+            "bundle_5":"0xf20505",
+            "bundle_6":"0x9ad909"
+        ]
+    }
+}

modules/nf-scil/bundle/coloring/tests/tags.yml

@@ -0,0 +1,2 @@
+bundle/coloring:
+  - "modules/nf-scil/bundle/coloring/**"