Add new module: flumut

modules/nf-core/flumut/run/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::flumut=0.6.5"

modules/nf-core/flumut/run/main.nf

@@ -0,0 +1,45 @@
+process FLUMUT_RUN {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "quay.io/biocontainers/flumut:0.6.5--pyhdfd78af_0"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    tuple val(meta), path("*.xlsm"), emit: xlsm
+
+    tuple val("${task.process}"), val('flumut'), eval("flumut --all-versions"), topic: versions, emit: versions_flumut
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    flumut \\
+        ${args} \\
+        -x ${prefix}.xlsm \\
+        -m ${prefix}_markers.tsv \\
+        -M ${prefix}_mutations.tsv \\
+        -l ${prefix}_literature.tsv \\
+        ${fasta}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch \\
+        ${prefix}.xlsm \\
+        ${prefix}_markers.tsv \\
+        ${prefix}_mutations.tsv \\
+        ${prefix}_literature.tsv
+    """
+}

modules/nf-core/flumut/run/meta.yml

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+name: "flumut_run"
+description: Run the FluMut tool to search for molecular markers with potential
+  impact on the biological characteristics of Influenza A viruses of the A(H5N1)
+  subtype.
+keywords:
+  - FluMut
+  - mutations
+  - surveillance
+  - H5N1
+  - Avian Influenza Virus
+tools:
+  - "flumut":
+      description: "A tool to search for molecular markers with potential impact on
+        the biological characteristics of Influenza A viruses of the A(H5N1) subtype."
+      homepage: "https://github.com/izsvenezie-virology/FluMut"
+      documentation: "https://izsvenezie-virology.github.io/FluMut/"
+      tool_dev_url: "https://github.com/izsvenezie-virology/FluMut"
+      doi: "10.1093/ve/veaf011"
+      licence:
+        - "AGPL v3-or-later"
+      identifier: biotools:flumut
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: The FASTA containing al the sequences to be analyzed
+        pattern: "*.{fa,fasta,fas}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+output:
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.tsv":
+          type: file
+          description: TSV files containing results
+          pattern: "*.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+  xlsm:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.xlsm":
+          type: file
+          description: Excel file containing results
+          pattern: "*.{xlsm}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3468"
+  versions_flumut:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - flumut:
+          type: string
+          description: The name of the tool
+      - flumut --all-versions:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - flumut:
+          type: string
+          description: The name of the tool
+      - flumut --all-versions:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@EdoardoGiussani"
+  - "@AlexSartori"
+maintainers:
+  - "@EdoardoGiussani"
+  - "@AlexSartori"

modules/nf-core/flumut/run/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process FLUMUT_RUN"
+    script "../main.nf"
+    process "FLUMUT_RUN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "flumut"
+    tag "flumut/run"
+
+    test("H5N1_2.3.4.4b_Italy - fasta") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/virus/influenza/fasta/H5N1_2.3.4.4b_Italy.fa', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.tsv,
+                    file(process.out.xlsm[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }
+            )
+        }
+
+    }
+
+    test("H5N1_2.3.4.4b_Italy - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/virus/influenza/fasta/H5N1_2.3.4.4b_Italy.fa', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/flumut/run/tests/main.nf.test.snap

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+{
+    "H5N1_2.3.4.4b_Italy - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_literature.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_markers.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_mutations.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "FLUMUT_RUN",
+                        "flumut",
+                        "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_literature.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_markers.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_mutations.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions_flumut": [
+                    [
+                        "FLUMUT_RUN",
+                        "flumut",
+                        "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17"
+                    ]
+                ],
+                "xlsm": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.xlsm:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-22T12:11:02.098163186",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    },
+    "H5N1_2.3.4.4b_Italy - fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "test_literature.tsv:md5,8999b029cb5cfcde7a4281cbcb3285c9",
+                        "test_markers.tsv:md5,cbdc33bff11829875d7a88c3bd8d0303",
+                        "test_mutations.tsv:md5,5c2d23a12a8fe807c237d952753daf3a"
+                    ]
+                ]
+            ],
+            "test.xlsm",
+            {
+                "versions_flumut": [
+                    [
+                        "FLUMUT_RUN",
+                        "flumut",
+                        "FluMut: 0.6.5\nFluMutDB: 6.6, released on 2026-03-17"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-05-22T12:10:54.114556478",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.04.6"
+        }
+    }
+}