Add the deacon/index tool.

modules/nf-core/deacon/index/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::deacon=0.5.0"

modules/nf-core/deacon/index/main.nf

@@ -0,0 +1,47 @@
+process DEACON_INDEX {
+    tag "$fasta"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/deacon:0.5.0--h4349ce8_0':
+        'biocontainers/deacon:0.5.0--h4349ce8_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.idx"), emit: index
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    deacon \\
+        index \\
+        build \\
+        --threads ${task.cpus} \\
+        $args \\
+        $fasta > ${prefix}.idx
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${fasta.baseName}"
+    """
+    touch ${prefix}.idx
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deacon: \$(deacon --version | head -n1 | sed 's/deacon //g')
+    END_VERSIONS
+    """
+}

modules/nf-core/deacon/index/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "deacon_index"
+description: Create deacon index for reference genome
+keywords:
+  - index
+  - fasta
+  - genome
+  - reference
+  - minimizer
+  - decontamination
+tools:
+  - "deacon":
+      description: "Fast alignment-free sequence filter"
+      homepage: "https://github.com/bede/deacon"
+      documentation: "https://github.com/bede/deacon#readme"
+      tool_dev_url: "https://github.com/bede/deacon"
+      doi: "10.1093/bioinformatics/btae004"
+      licence: ["MIT"]
+      identifier: "biotools:deacon"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing reference information.
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+        pattern: "*.{fasta,fasta.gz,fas,fas.gz,fa,fa.gz,fna,fna.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/data_2044" # Sequence
+          - edam: "http://edamontology.org/format_1929" # FASTA
+
+output:
+  - index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing reference information.
+            e.g. [ id:'test', single_end:false ]
+      - "*.idx":
+          type: file
+          description: Deacon minimizer index file
+          pattern: "*.idx"
+          ontologies:
+            - edam: "http://edamontology.org/data_3210" # Genome index
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@mberacochea"
+maintainers:
+  - "@mberacochea"

modules/nf-core/deacon/index/tests/main.nf.test

@@ -0,0 +1,88 @@
+nextflow_process {
+
+    name "Test Process DEACON_INDEX"
+    script "../main.nf"
+    process "DEACON_INDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "deacon"
+    tag "deacon/index"
+
+    test("index sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        process.out.index,
+                        process.out.versions.collect { path(it).yaml }
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("index sarscov2 - fasta gzipped") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("index sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/deacon/index/tests/main.nf.test.snap

@@ -0,0 +1,106 @@
+{
+    "index sarscov2 - fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                ]
+            ],
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-16T08:54:38.622063"
+    },
+    "index sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.idx:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
+                ]
+            },
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-16T12:31:10.825365"
+    },
+    "index sarscov2 - fasta gzipped": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.idx:md5,7437b25e6659ebfd5cf9be7b325f90c3"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,60749febc4eaab16229dc078af00ea27"
+                ]
+            },
+            [
+                {
+                    "DEACON_INDEX": {
+                        "deacon": "0.5.0"
+                    }
+                }
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.3"
+        },
+        "timestamp": "2025-06-16T12:31:07.212408"
+    }
+}