[WIP]: add module tensor

modules/nf-neuro/tensor/ratio/environment.yml

@@ -0,0 +1,6 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "tensor_ratio"
+channels: []
+dependencies: []
+

modules/nf-neuro/tensor/ratio/main.nf

@@ -0,0 +1,48 @@
+process TENSOR_RATIO {
+    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:latest' }"
+
+    input:
+        tuple val(meta), path(image)
+
+    output:
+        tuple val(meta), path("*_Dxx_to_Dyy.nii.gz")        , emit: tensor_x_to_y
+        tuple val(meta), path("*_Dxx_to_Dzz.nii.gz")        , emit: tensor_x_to_z
+        path "versions.yml"                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    fslsplit $image
+    fslmaths ${image}_0000.nii.gz -div ${image}_0003.nii.gz ${prefix}_Dxx_to_Dyy.nii.gz
+    fslmaths ${image}_0000.nii.gz -div ${image}_0005.nii.gz ${prefix}_Dxx_to_Dzz.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fsl: \$(fslsplit -version 2>&1 | sed -n 's/FSLSPLIT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}_Dxx_to_Dyy.nii.gz
+    touch ${prefix}_Dxx_to_Dzz.nii.gz
+    fslsplit
+    fslmaths
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fsl: \$(fslsplit -version 2>&1 | sed -n 's/FSLSPLIT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}

modules/nf-neuro/tensor/ratio/meta.yml

@@ -0,0 +1,51 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "tensor_ratio"
+description: Split the tensor image and compute the ratio of Dxx to Dyy and Dxx to Dzz for ALPS.
+keywords:
+  - DWI
+  - tensor
+  - DTI-ALPS
+tools:
+  - "FSL":
+      description: "FSL Toolbox"
+      homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti tensor image volume to extract Dx to Dy and Dx to Dz.
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - tensor_x_to_y:
+      type: file
+      description: Nifti volume ratio of Dxx to Dyy.
+      pattern: "*_Dxx_to_Dyy.{nii,nii.gz}"
+
+  - tensor_x_to_z:
+      type: file
+      description: Nifti volume ratio of Dxx to Dzz.
+      pattern: "*_Dxx_to_Dzz.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@atsuch"
+maintainers:
+  - "@atsuch"

modules/nf-neuro/tensor/ratio/tests/main.nf.test

@@ -0,0 +1,78 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test tensor/ratio
+nextflow_process {
+
+    name "Test Process TENSOR_RATIO"
+    script "../main.nf"
+    process "TENSOR_RATIO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tensor"
+    tag "tensor/ratio"
+
+    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( [ "dti.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+    test("tensorratio - classic") {
+        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}/dti/tensor.nii.gz")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("tensorratio - stub") {
+
+        options "-stub"
+
+        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}/dti/tensor.nii.gz")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-neuro/tensor/ratio/tests/main.nf.test.snap

@@ -0,0 +1,60 @@
+{
+    "tensorratio - classic": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "tensor_x_to_y": [
+
+                ],
+                "tensor_x_to_z": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-27T14:05:10.553221131"
+    },
+    "tensorratio - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "tensor_x_to_y": [
+
+                ],
+                "tensor_x_to_z": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-27T14:05:28.311339916"
+    }
+}

modules/nf-neuro/tensor/ratio/tests/tags.yml

@@ -0,0 +1,2 @@
+tensor/ratio:
+  - "modules/nf-neuro/tensor/ratio/**"