[WIP] Add module connectivity visualization

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

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+---
+channels: []
+dependencies: []
+name: connectivity_visualize

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

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+process CONNECTIVITY_VISUALIZE {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ 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(matrices), path (atlas_labels), path(labels_list)
+
+    output:
+    tuple val(meta), path("*.png"), emit: figure
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+
+    String matrices_list = matrices.join(", ").replace(',', '')
+    def name_axis = task.ext.name_axis ? "--name_axis " : ""
+    def display_legend = task.ext.display_legend ? "--display_legend " : ""
+    def exclude_zeros = task.ext.exclude_zeros ? "--exclude_zeros " : ""
+    def nb_bins = task.ext.nb_bins ? "--nb_bins " + task.ext.nb_bins : "--nb_bins 50"
+    def axis_text_size = task.ext.axis_text_size ? "--axis_text_size $task.ext.axis_text_size $task.ext.axis_text_size" : "--axis_text_size 5 5"
+    def args = ""
+    if (atlas_labels) args += [" --lookup_table $atlas_labels "]
+    if (labels_list) args += [" --name_axis "]
+
+    """
+    for matrix in $matrices_list; do
+        scil_viz_connectivity.py \$matrix \${matrix/.npy/_matrix.png} \
+            $name_axis $display_legend --histogram \${matrix/.npy/_histogram.png} \
+            $nb_bins $exclude_zeros $axis_text_size \
+            $args
+    done
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    String  matrices_list = matrices.join(", ").replace(',', '')
+    """
+    for metric in $matrices_list; do
+        base_name=\$(basename "\${metric}" .npy)
+        touch "\${base_name}.png"
+    done
+
+    scil_viz_connectivity.py -h
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}

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

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+---
+name: "connectivity_visualize"
+description: display a connectivity matrix and adjust the desired visualization.
+keywords:
+  - numpy
+  - connectivity
+  - visualize
+  - 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 ]`
+
+  - matrices:
+      type: file
+      description: List of connectivity matrices. the set of matrices is concatenated into a single matrix, but can also contain a single matrix.
+      pattern: "*.npy"
+
+  - atlas_labels:
+      type: file
+      description: Lookup table with the label number as keys and the name as values
+      pattern: "*.json"
+
+  - labels_list:
+      type: file
+      description: List saved by the decomposition script, must contain labels rather than coordinates.
+      pattern: "*.txt"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - figure:
+      type: file
+      description: Output filename for the connectivity matrix figure.
+      pattern: "*.png"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"
+maintainers:
+  - "@ThoumyreStanislas"

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

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+nextflow_process {
+
+    name "Test Process CONNECTIVITY_VISUALIZE"
+    script "../main.nf"
+    process "CONNECTIVITY_VISUALIZE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "connectivity"
+    tag "connectivity/visualize"
+
+    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 - visualisation ") {
+        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}/*.npy", checkIfExists: true),
+                        [],
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+        test("connectivity - visualisation - stub-run") {
+        options "-stub-run"
+        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}/*.npy", checkIfExists: true),
+                        [],
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,111 @@
+{
+    "connectivity - visualisation ": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "afd_max_histogram.png:md5,43912780c2ac709b631fc39d95d464e8",
+                            "afd_max_matrix.png:md5,89adc0462e5f6ee412110994e6e6b3eb",
+                            "len_histogram.png:md5,117651740e19ee3c536c9a4bea6babfb",
+                            "len_matrix.png:md5,e2098003d452ce2ba9db2c265d8516e9",
+                            "mask_histogram.png:md5,073e208a8a327baa5bbf721e66e337d4",
+                            "mask_matrix.png:md5,ec19ecce53d485ca983bf17bc87b56c7",
+                            "pval_histogram.png:md5,892ebc7b367db2ac1bd970f638043904",
+                            "pval_matrix.png:md5,2b8e9a9f8833110d7a2f9d612ae6f2be",
+                            "sc_add_10_histogram.png:md5,265a9399387c856977eae1ea3f83516a",
+                            "sc_add_10_matrix.png:md5,07e322fd583f9b8235c50363d7aba9e0",
+                            "sc_histogram.png:md5,7baccf0dc5a650bea2aecd19d3867653",
+                            "sc_lower_threshold_histogram.png:md5,cd4368e81ef4f9f128a444a7897d0c1e",
+                            "sc_lower_threshold_matrix.png:md5,748d5a2a15159896775ebb7aa71a3fd5",
+                            "sc_masked_histogram.png:md5,2a0163a153ee2b3174138ba4505ec6fb",
+                            "sc_masked_matrix.png:md5,1b52240fc505e2e002c65b9e4f0ce777",
+                            "sc_matrix.png:md5,db388963daf62fae2ef1d8be58c9cad8",
+                            "sc_norm_histogram.png:md5,bfc9fa64063f6a8797f3bb49d2bfcbfd",
+                            "sc_norm_matrix.png:md5,67ef585c7559edb6e7c88ca50304db4f",
+                            "sc_norm_vol_histogram.png:md5,1eb857ea304f82fe73bc3a6416ade1d1",
+                            "sc_norm_vol_matrix.png:md5,572daf7d844699f96cc1519458491f3b",
+                            "sc_normalize_histogram.png:md5,dbc8741adf4dd3a597199c36a9ed197d",
+                            "sc_normalize_matrix.png:md5,2bc762a0e4861d726bbec1372b124763",
+                            "sc_reo_fake_histogram.png:md5,1f2efba6ff6a949f6bdc9b07e3d0952b",
+                            "sc_reo_fake_matrix.png:md5,2d8e4abada02b7d096e38888a2ea2a09",
+                            "sc_thr_histogram.png:md5,cd4368e81ef4f9f128a444a7897d0c1e",
+                            "sc_thr_matrix.png:md5,748d5a2a15159896775ebb7aa71a3fd5",
+                            "sim_histogram.png:md5,e82b14b3fbb8184e53265a05fe247fd0",
+                            "sim_matrix.png:md5,e42c85fbd2211738bb38882305122c9a",
+                            "vol_histogram.png:md5,5b60e61f931294416a22ad3a7d8848ca",
+                            "vol_matrix.png:md5,85ddd42c1562adaf38aee0cc32334039"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3114f700c3813ee15388713fe8a539f1"
+                ],
+                "figure": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "afd_max_histogram.png:md5,43912780c2ac709b631fc39d95d464e8",
+                            "afd_max_matrix.png:md5,89adc0462e5f6ee412110994e6e6b3eb",
+                            "len_histogram.png:md5,117651740e19ee3c536c9a4bea6babfb",
+                            "len_matrix.png:md5,e2098003d452ce2ba9db2c265d8516e9",
+                            "mask_histogram.png:md5,073e208a8a327baa5bbf721e66e337d4",
+                            "mask_matrix.png:md5,ec19ecce53d485ca983bf17bc87b56c7",
+                            "pval_histogram.png:md5,892ebc7b367db2ac1bd970f638043904",
+                            "pval_matrix.png:md5,2b8e9a9f8833110d7a2f9d612ae6f2be",
+                            "sc_add_10_histogram.png:md5,265a9399387c856977eae1ea3f83516a",
+                            "sc_add_10_matrix.png:md5,07e322fd583f9b8235c50363d7aba9e0",
+                            "sc_histogram.png:md5,7baccf0dc5a650bea2aecd19d3867653",
+                            "sc_lower_threshold_histogram.png:md5,cd4368e81ef4f9f128a444a7897d0c1e",
+                            "sc_lower_threshold_matrix.png:md5,748d5a2a15159896775ebb7aa71a3fd5",
+                            "sc_masked_histogram.png:md5,2a0163a153ee2b3174138ba4505ec6fb",
+                            "sc_masked_matrix.png:md5,1b52240fc505e2e002c65b9e4f0ce777",
+                            "sc_matrix.png:md5,db388963daf62fae2ef1d8be58c9cad8",
+                            "sc_norm_histogram.png:md5,bfc9fa64063f6a8797f3bb49d2bfcbfd",
+                            "sc_norm_matrix.png:md5,67ef585c7559edb6e7c88ca50304db4f",
+                            "sc_norm_vol_histogram.png:md5,1eb857ea304f82fe73bc3a6416ade1d1",
+                            "sc_norm_vol_matrix.png:md5,572daf7d844699f96cc1519458491f3b",
+                            "sc_normalize_histogram.png:md5,dbc8741adf4dd3a597199c36a9ed197d",
+                            "sc_normalize_matrix.png:md5,2bc762a0e4861d726bbec1372b124763",
+                            "sc_reo_fake_histogram.png:md5,1f2efba6ff6a949f6bdc9b07e3d0952b",
+                            "sc_reo_fake_matrix.png:md5,2d8e4abada02b7d096e38888a2ea2a09",
+                            "sc_thr_histogram.png:md5,cd4368e81ef4f9f128a444a7897d0c1e",
+                            "sc_thr_matrix.png:md5,748d5a2a15159896775ebb7aa71a3fd5",
+                            "sim_histogram.png:md5,e82b14b3fbb8184e53265a05fe247fd0",
+                            "sim_matrix.png:md5,e42c85fbd2211738bb38882305122c9a",
+                            "vol_histogram.png:md5,5b60e61f931294416a22ad3a7d8848ca",
+                            "vol_matrix.png:md5,85ddd42c1562adaf38aee0cc32334039"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3114f700c3813ee15388713fe8a539f1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T10:54:29.917241635"
+    },
+    "connectivity - visualisation - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,3114f700c3813ee15388713fe8a539f1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T10:55:34.856253711"
+    }
+}

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

@@ -0,0 +1,10 @@
+process {
+    withName: "CONNECTIVITY_VISUALIZE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.name_axis = true
+        ext.display_legend = true
+        ext.exclude_zeros = true
+        ext.ext.nb_bins = 50
+        ext.axis_text_size = 5
+    }
+}

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

@@ -0,0 +1,2 @@
+connectivity/visualize:
+  - "modules/nf-neuro/connectivity/visualize/**"