Add the finaletoolkit/delfi module

modules/nf-core/finaletoolkit/delfi/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::finaletoolkit=0.11.1"

modules/nf-core/finaletoolkit/delfi/main.nf

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+process FINALETOOLKIT_DELFI {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34f01d128ed135aedc33ddb62fced3911bef6d1a909694291b7184bf83719402/data'
+        : 'community.wave.seqera.io/library/finaletoolkit:0.11.1--8fe5ba6ec9e2ec95'}"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    tuple val(meta2), path(genome_2bit)
+    tuple val(meta3), path(chromosome_sizes)
+    tuple val(meta4), path(bins)
+
+    output:
+    tuple val(meta), path("*.bed"), emit: bed
+    tuple val("${task.process}"), val('finaletoolkit'), eval("finaletoolkit --version | sed 's/FinaleToolkit //g'"), topic: versions, emit: versions_finaletoolkit
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    finaletoolkit \\
+        delfi \\
+        -w ${task.cpus} \\
+        ${bam} \\
+        ${chromosome_sizes} \\
+        ${genome_2bit} \\
+        ${bins} \\
+        ${args} \\
+        -o "${prefix}_delfi.bed"
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}_delfi.bed
+    """
+}

modules/nf-core/finaletoolkit/delfi/meta.yml

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+name: "finaletoolkit_delfi"
+description: Generate a binned fragment profile and a fragment distribution histogram
+keywords:
+  - sort
+  - genomics
+  - fragmentomics
+tools:
+  - "finaletoolkit":
+      description: "Extract cfDNA fragmentation features from sequencing data."
+      homepage: "https://epifluidlab.github.io/FinaleToolkit/"
+      documentation: "https://epifluidlab.github.io/FinaleToolkit/documentation/index.html"
+      tool_dev_url: "https://github.com/epifluidlab/FinaleToolkit"
+      doi: "10.1093/bioadv/vbaf236"
+      licence:
+        - "MIT"
+      identifier: biotools:finaletoolkit
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.bam"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572"
+    - bai:
+        type: file
+        description: BAM file index
+        pattern: "*.bai"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - genome_2bit:
+        type: file
+        description: |
+          2bit compressed genome file (must be the same as the one used for the
+          BAM file)
+        pattern: "*.2bit"
+        ontologies:
+          - edam: "http://edamontology.org/format_3009"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - chromosome_sizes:
+        type: file
+        pattern: "*.sizes"
+        description: |
+          Two-column file containing the size for each chromosome
+        ontologies:
+          - edam: "http://edamontology.org/format_3475"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bins:
+        type: file
+        description: |
+          BED containing binned genomic coordinates
+        pattern: "*.bed"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
+output:
+  bed:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.bed":
+          type: file
+          pattern: "*.bed"
+          description: |
+            BED file containing DELFI scores
+          ontologies:
+            - edam: "http://edamontology.org/format_3003"
+  versions_finaletoolkit:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - finaletoolkit:
+          type: string
+          description: The name of the tool
+      - "finaletoolkit --version | sed 's/FinaleToolkit //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - finaletoolkit:
+          type: string
+          description: The name of the tool
+      - "finaletoolkit --version | sed 's/FinaleToolkit //g'":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@lbeltrame"
+maintainers:
+  - "@lbeltrame"

modules/nf-core/finaletoolkit/delfi/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process FINALETOOLKIT_DELFI"
+    script "../main.nf"
+    process "FINALETOOLKIT_DELFI"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "finaletoolkit"
+    tag "finaletoolkit/delfi"
+
+    test("homo_sapiens - bam") {
+
+        when {
+
+            process {
+
+                config "./nextflow.config"
+
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam.bai', checkIfExists: true),
+                ]
+                input[1] = [
+                    [id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true)
+                    ,
+                ]
+                input[2] = [
+                    [id: 'sizes' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.sizes', checkIfExists: true),
+                ]
+                input[3] = [
+                    [id: 'bins' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bins_10kb.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - stub") {
+
+        options "-stub"
+
+        when {
+
+            process {
+
+                config "./nextflow.config"
+
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam.bai', checkIfExists: true),
+                ]
+                input[1] = [
+                    [id: 'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.2bit', checkIfExists: true)
+                    ,
+                ]
+                input[2] = [
+                    [id: 'sizes' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.sizes', checkIfExists: true),
+                ]
+                input[3] = [
+                    [id: 'bins' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bins_10kb.bed', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/finaletoolkit/delfi/tests/main.nf.test.snap

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+{
+    "homo_sapiens - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_delfi.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_delfi.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_finaletoolkit": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ]
+            },
+            {
+                "versions_finaletoolkit": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-06T14:45:08.530570524"
+    },
+    "homo_sapiens - bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_delfi.bed:md5,125dc88e57b66bf668a8961c81ede4a8"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_delfi.bed:md5,125dc88e57b66bf668a8961c81ede4a8"
+                    ]
+                ],
+                "versions_finaletoolkit": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ]
+            },
+            {
+                "versions_finaletoolkit": [
+                    [
+                        "FINALETOOLKIT_DELFI",
+                        "finaletoolkit",
+                        "0.11.1"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
+        },
+        "timestamp": "2026-05-07T08:54:00.659731417"
+    }
+}

modules/nf-core/finaletoolkit/delfi/tests/nextflow.config

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+process {
+    withName: 'FINALETOOLKIT_DELFI' {
+        // Chr22 is too small for meaningful data, so remove all filters
+        // We need 2 workers because otherwise there is a bug (fixed upstream, but without a new version)
+        // that breaks the program with only one worker
+        cpus = 2
+        ext.args = "--no-merge-bins --no-gc-correct --quality-threshold 0"
+    }
+}