Add module stainwarpy/transformsegmask

modules/nf-core/stainwarpy/transformsegmask/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::stainwarpy=0.2.3

modules/nf-core/stainwarpy/transformsegmask/main.nf

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+process STAINWARPY_TRANSFORMSEGMASK {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/stainwarpy:0.2.3--5966e23f2f7d254a' :
+        'community.wave.seqera.io/library/stainwarpy:0.2.3--2c8b18a5e6d93e4a'}"
+
+    input:
+    tuple val(meta), path(hne_img)
+    tuple val(meta2), path(multiplx_img)
+    tuple val(meta3), path(seg_mask)
+    tuple val(meta4), path(tform_map)
+    val fixed_img
+    val final_sz
+
+    output:
+    tuple val(meta), path("transformed_segmentation_mask.ome.tif")     , emit: transformed_seg_mask
+    tuple val("${task.process}"), val('stainwarpy'), eval("stainwarpy --version | sed 's/.* //'"), emit: versions_stainwarpy_transformsegmask, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    stainwarpy \\
+        transform-seg-mask \\
+        ${seg_mask} \\
+        ${multiplx_img} \\
+        ${hne_img} \\
+        . \\
+        ${tform_map} \\
+        ${fixed_img} \\
+        ${final_sz} \\
+        ${args}
+    """
+
+    stub:
+
+    """
+    touch transformed_segmentation_mask.ome.tif
+    """
+}

modules/nf-core/stainwarpy/transformsegmask/meta.yml

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+name: "stainwarpy_transformsegmask"
+description: Transform segmentation mask of multiplexed or H&E stained tissue images using stainwarpy
+keywords:
+  - image registration
+  - histology
+  - hne
+  - multiplexed
+  - segmentation mask
+tools:
+  - "stainwarpy":
+      description: "Register H&E stained and Multiplexed tissue images using feature-based image registration"
+      homepage: "https://github.com/tckumarasekara/stainwarpy"
+      documentation: "https://github.com/tckumarasekara/stainwarpy"
+      tool_dev_url: "https://github.com/tckumarasekara/stainwarpy"
+      licence: ["MIT License", "Apache-2.0"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - hne_img:
+        type: file
+        description: H&E stained image file
+        pattern: "*.{ome.tif,ome.tiff,tif,tiff}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3727"
+          - edam: "http://edamontology.org/format_3591"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - multiplx_img:
+        type: file
+        description: Multiplexed image file
+        pattern: "*.{ome.tif,ome.tiff,tif,tiff}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3727"
+          - edam: "http://edamontology.org/format_3591"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - seg_mask:
+        type: file
+        description: Segmentation mask file
+        pattern: "*.{ome.tif,ome.tiff,tif,tiff,npy}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3727"
+          - edam: "http://edamontology.org/format_3591"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - tform_map:
+        type: file
+        description: Transformation map file
+        pattern: "*.npy"
+        ontologies: []
+  - fixed_img:
+      type: string
+      description: Which image to use as fixed image for registration. Options - 'hne' or 'multiplexed'
+      ontologies: []
+  - final_sz:
+      type: string
+      description: In which pixel size to output the registered image and segmentation mask. Options - 'hne' or 'multiplexed'
+      ontologies: []
+
+output:
+  transformed_seg_mask:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "transformed_segmentation_mask.ome.tif":
+          type: file
+          description: Transformed segmentation mask in OME-TIFF format
+          pattern: "transformed_segmentation_mask.ome.tif"
+          ontologies:
+            - edam: "http://edamontology.org/format_3727"
+  versions_stainwarpy_transformsegmask:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "stainwarpy":
+          type: string
+          description: The name of the tool
+      - "stainwarpy --version | sed 's/.* //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - stainwarpy:
+          type: string
+          description: The name of the tool
+      - stainwarpy --version | sed 's/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@tckumarasekara"
+maintainers:
+  - "@tckumarasekara"

modules/nf-core/stainwarpy/transformsegmask/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process STAINWARPY_TRANSFORMSEGMASK"
+    script "../main.nf"
+    process "STAINWARPY_TRANSFORMSEGMASK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stainwarpy"
+    tag "stainwarpy/transformsegmask"
+
+    config "./nextflow.config"
+
+    test("colon_tissue_local - ome.tif") {
+
+        when {
+            params {
+                modules_args = ""
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/hne_image_colon.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/multiplexed_single_channel_img.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/hne_segmentation_mask.ome.tif', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/feature_based_transformation_map.npy', checkIfExists: true)
+                ]
+                input[4] = 'multiplexed'
+                input[5] = 'multiplexed'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.transformed_seg_mask.get(0).get(1)).exists(),
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("colon_tissue_local - ome.tif - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                modules_args = null
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/hne_image_colon.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/multiplexed_single_channel_img.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/hne_segmentation_mask.ome.tif', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'sample1'],
+                    file(params.modules_testdata_base_path + 'imaging/hne_multiplexed/feature_based_transformation_map.npy', checkIfExists: true)
+                ]
+                input[4] = 'multiplexed'
+                input[5] = 'multiplexed'
+                """
+            }
+        }
+
+        then {
+            { assert snapshot(
+                    process.out.transformed_seg_mask,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+        }
+
+    }
+
+}

modules/nf-core/stainwarpy/transformsegmask/tests/main.nf.test.snap

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+{
+    "colon_tissue_local - ome.tif": {
+        "content": [
+            true,
+            {
+                "versions_stainwarpy_transformsegmask": [
+                    [
+                        "STAINWARPY_TRANSFORMSEGMASK",
+                        "stainwarpy",
+                        "0.2.3"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-20T13:38:10.728598964"
+    },
+    "colon_tissue_local - ome.tif - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "sample1"
+                    },
+                    "transformed_segmentation_mask.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            {
+                "versions_stainwarpy_transformsegmask": [
+                    [
+                        "STAINWARPY_TRANSFORMSEGMASK",
+                        "stainwarpy",
+                        "0.2.3"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-20T13:38:17.92763081"
+    }
+}

modules/nf-core/stainwarpy/transformsegmask/tests/nextflow.config

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+process {
+    withName: STAINWARPY_TRANSFORMSEGMASK {
+        ext.args = params.modules_args ?: ''
+    }
+}