diff --git a/modules/nf-core/macsyfinder/download/environment.yml b/modules/nf-core/macsyfinder/download/environment.yml
new file mode 100644
index 00000000000..7feab3433e4
--- /dev/null
+++ b/modules/nf-core/macsyfinder/download/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::macsyfinder=2.1.6
diff --git a/modules/nf-core/macsyfinder/download/main.nf b/modules/nf-core/macsyfinder/download/main.nf
new file mode 100644
index 00000000000..6969294a3c7
--- /dev/null
+++ b/modules/nf-core/macsyfinder/download/main.nf
@@ -0,0 +1,39 @@
+process MACSYFINDER_DOWNLOAD {
+    tag "${model_name}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/macsyfinder:2.1.6--pyhdfd78af_0' :
+        'biocontainers/macsyfinder:2.1.6--pyhdfd78af_0' }"
+
+    input:
+    val model_name
+
+    output:
+    path "models"       , emit: models
+    tuple val("${task.process}"), val('macsyfinder'), eval('macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//"'), topic: versions, emit: versions_macsyfinder
+    tuple val("${task.process}"), val('msf_data'), eval('msf_data --version 2>&1 | awk "NR==4" | sed "s/^- MacSyLib //;s/ *$//"'), topic: versions, emit: versions_macsydata
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    # msf_data installs models into the current directory by default
+    # We'll create a models directory to store them
+    mkdir -p models
+
+    msf_data install \\
+        --target models \\
+        ${args} \\
+        ${model_name}
+    """
+
+    stub:
+    """
+    mkdir -p models/${model_name}
+    touch models/${model_name}/definitions.txt
+    """
+}
diff --git a/modules/nf-core/macsyfinder/download/meta.yml b/modules/nf-core/macsyfinder/download/meta.yml
new file mode 100644
index 00000000000..66a1f0c41fa
--- /dev/null
+++ b/modules/nf-core/macsyfinder/download/meta.yml
@@ -0,0 +1,73 @@
+name: "macsyfinder_download"
+description: Download MacSyFinder models using msf_data
+keywords:
+  - genomics
+  - protein
+  - macromolecular systems
+  - models
+  - database
+tools:
+  - "macsyfinder":
+      description: "Detection of macromolecular systems in protein datasets using systems\
+        \ modelling and similarity search"
+      homepage: "https://github.com/gem-pasteur/macsyfinder"
+      documentation: "https://macsyfinder.readthedocs.io"
+      tool_dev_url: "https://github.com/gem-pasteur/macsyfinder"
+      doi: "10.24072/pcjournal.250"
+      licence:
+        - "GPL v3"
+      identifier: biotools:macsyfinder
+input:
+  - model_name:
+      type: string
+      description: Name of the MacSyFinder model to download (e.g., 'TXSScan', 'CasFinder')
+output:
+  models:
+    - models:
+        type: directory
+        description: Directory containing downloaded MacSyFinder model definitions
+        pattern: "models"
+  versions_macsyfinder:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_macsydata:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - msf_data:
+          type: string
+          description: The name of the tool
+      - msf_data --version 2>&1 | awk "NR==4" | sed "s/^- MacSyLib //;s/ *$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - msf_data:
+          type: string
+          description: The name of the tool
+      - msf_data --version 2>&1 | awk "NR==4" | sed "s/^- MacSyLib //;s/ *$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@brovolia"
+maintainers:
+  - "@brovolia"
diff --git a/modules/nf-core/macsyfinder/download/tests/main.nf.test b/modules/nf-core/macsyfinder/download/tests/main.nf.test
new file mode 100644
index 00000000000..e458f4c43a5
--- /dev/null
+++ b/modules/nf-core/macsyfinder/download/tests/main.nf.test
@@ -0,0 +1,54 @@
+nextflow_process {
+
+    name "Test Process MACSYFINDER_DOWNLOAD"
+    script "../main.nf"
+    process "MACSYFINDER_DOWNLOAD"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "macsyfinder"
+    tag "macsyfinder/download"
+
+    test("macsyfinder_download - TXSScan") {
+
+        when {
+            process {
+                """
+                input[0] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.models.collect { file(it).name },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
+    test("macsyfinder_download - TXSScan - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.models.collect { file(it).name },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/macsyfinder/download/tests/main.nf.test.snap b/modules/nf-core/macsyfinder/download/tests/main.nf.test.snap
new file mode 100644
index 00000000000..461d3f382d3
--- /dev/null
+++ b/modules/nf-core/macsyfinder/download/tests/main.nf.test.snap
@@ -0,0 +1,58 @@
+{
+    "macsyfinder_download - TXSScan": {
+        "content": [
+            [
+                "models"
+            ],
+            {
+                "versions_macsydata": [
+                    [
+                        "MACSYFINDER_DOWNLOAD",
+                        "msf_data",
+                        "1.0.4"
+                    ]
+                ],
+                "versions_macsyfinder": [
+                    [
+                        "MACSYFINDER_DOWNLOAD",
+                        "macsyfinder",
+                        "2.1.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-27T17:06:58.95757876"
+    },
+    "macsyfinder_download - TXSScan - stub": {
+        "content": [
+            [
+                "models"
+            ],
+            {
+                "versions_macsydata": [
+                    [
+                        "MACSYFINDER_DOWNLOAD",
+                        "msf_data",
+                        "1.0.4"
+                    ]
+                ],
+                "versions_macsyfinder": [
+                    [
+                        "MACSYFINDER_DOWNLOAD",
+                        "macsyfinder",
+                        "2.1.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-27T17:07:09.322980182"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/macsyfinder/search/environment.yml b/modules/nf-core/macsyfinder/search/environment.yml
new file mode 100644
index 00000000000..7feab3433e4
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::macsyfinder=2.1.6
diff --git a/modules/nf-core/macsyfinder/search/main.nf b/modules/nf-core/macsyfinder/search/main.nf
new file mode 100644
index 00000000000..2fbeb2e80c0
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/main.nf
@@ -0,0 +1,59 @@
+process MACSYFINDER_SEARCH {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/macsyfinder:2.1.6--pyhdfd78af_0' :
+        'biocontainers/macsyfinder:2.1.6--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(proteins)
+    path models
+    val model_names
+
+    output:
+    tuple val(meta), path("${prefix}/*")                    , emit: results
+    tuple val(meta), path("${prefix}/hmmer_results")        , emit: hmmer    , optional: true
+    tuple val(meta), path("${prefix}/macsyfinder.out")      , emit: stdout   , optional: true
+    tuple val(meta), path("${prefix}/macsyfinder.err")      , emit: stderr   , optional: true
+    tuple val(meta), path("${prefix}/all_systems.tsv")      , emit: summary  , optional: true
+    tuple val(meta), path("${prefix}/all_best_solutions*")  , emit: best_solutions, optional: true
+    tuple val("${task.process}"), val('macsyfinder'), eval('macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//"'), topic: versions, emit: versions_macsyfinder
+    tuple val("${task.process}"), val('hmmer'), eval('hmmsearch -h 2>&1 | sed "2!d;s/^# HMMER //;s/ .*$//"'), topic: versions, emit: versions_hmmer
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def model_arg = model_names ? "--models ${model_names}" : ""
+    """
+    macsyfinder \\
+        --sequence-db ${proteins} \\
+        --models-dir ${models} \\
+        ${model_arg} \\
+        --out-dir ${prefix} \\
+        --worker ${task.cpus} \\
+        ${args} \\
+        2>| >( tee macsyfinder.err >&2 ) \\
+        | tee macsyfinder.out
+
+    mv macsyfinder.err ${prefix}/
+    mv macsyfinder.out ${prefix}/
+
+    # Remove empty error files to avoid snapshot pollution
+    find ${prefix} -name "*.err" -type f -size 0 -delete
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}
+    touch ${prefix}/macsyfinder.err
+    touch ${prefix}/macsyfinder.out
+    touch ${prefix}/all_systems.tsv
+    touch ${prefix}/all_best_solutions.txt
+    """
+}
diff --git a/modules/nf-core/macsyfinder/search/meta.yml b/modules/nf-core/macsyfinder/search/meta.yml
new file mode 100644
index 00000000000..31a477b1069
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/meta.yml
@@ -0,0 +1,149 @@
+name: "macsyfinder_search"
+description: Search for macromolecular systems in protein datasets using MacSyFinder
+keywords:
+  - genomics
+  - protein
+  - macromolecular systems
+  - hmmer
+  - search
+tools:
+  - "macsyfinder":
+      description: "Detection of macromolecular systems in protein datasets using systems\
+        \ modelling and similarity search"
+      homepage: "https://github.com/gem-pasteur/macsyfinder"
+      documentation: "https://macsyfinder.readthedocs.io"
+      tool_dev_url: "https://github.com/gem-pasteur/macsyfinder"
+      doi: "10.24072/pcjournal.250"
+      licence:
+        - "GPL v3"
+      identifier: biotools:macsyfinder
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test' ]`
+    - proteins:
+        type: file
+        description: Protein sequence file in FASTA format
+        pattern: "*.{fasta,faa,fa}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929"
+  - models:
+      type: directory
+      description: Directory containing MacSyFinder model(s)
+      pattern: "*"
+  - model_names:
+      type: string
+      description: Space-separated list of model names to search for. If not provided,
+        all models in the directory will be used.
+output:
+  results:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/*:
+          type: directory
+          description: Directory containing all MacSyFinder results
+          pattern: "${prefix}/*"
+  hmmer:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/hmmer_results:
+          type: directory
+          description: Directory containing HMMER search results (may contain variable content like timestamps)
+          pattern: "${prefix}/hmmer_results"
+  stdout:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/macsyfinder.out:
+          type: file
+          description: MacSyFinder standard output
+          pattern: "${prefix}/macsyfinder.out"
+          ontologies: []
+  stderr:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/macsyfinder.err:
+          type: file
+          description: MacSyFinder standard error
+          pattern: "${prefix}/macsyfinder.err"
+          ontologies: []
+  summary:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/all_systems.tsv:
+          type: file
+          description: Summary table of all detected systems
+          pattern: "${prefix}/all_systems.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475"
+  best_solutions:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', db_type:'gembase' ]`
+      - ${prefix}/all_best_solutions*:
+          type: file
+          description: Best solution files for detected systems
+          pattern: "${prefix}/all_best_solutions*"
+          ontologies: []
+  versions_macsyfinder:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_hmmer:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hmmer:
+          type: string
+          description: The name of the tool
+      - hmmsearch -h 2>&1 | sed "2!d;s/^# HMMER //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - macsyfinder:
+          type: string
+          description: The name of the tool
+      - macsyfinder --version 2>&1 | sed "1!d;s/^.*MacSyFinder //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hmmer:
+          type: string
+          description: The name of the tool
+      - hmmsearch -h 2>&1 | sed "2!d;s/^# HMMER //;s/ .*$//":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@brovolia"
+maintainers:
+  - "@brovolia"
diff --git a/modules/nf-core/macsyfinder/search/tests/main.nf.test b/modules/nf-core/macsyfinder/search/tests/main.nf.test
new file mode 100644
index 00000000000..c508e726cb9
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/tests/main.nf.test
@@ -0,0 +1,127 @@
+nextflow_process {
+
+    name "Test Process MACSYFINDER_SEARCH"
+    script "../main.nf"
+    process "MACSYFINDER_SEARCH"
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "macsyfinder"
+    tag "macsyfinder/search"
+    tag "macsyfinder/download"
+    tag "pigz"
+    tag "pigz/compress"
+
+    setup {
+        run("MACSYFINDER_DOWNLOAD") {
+            script "../../download/main.nf"
+            process {
+                """
+                input[0] = 'TXSScan'
+                """
+            }
+        }
+    }
+
+    test("macsyfinder_search - proteins - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
+                ]
+                input[1] = MACSYFINDER_DOWNLOAD.out.models
+                input[2] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.best_solutions.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stderr.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stdout.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.summary.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
+    test("macsyfinder_search - proteins - fasta.gz") {
+
+        setup {
+            run("PIGZ_COMPRESS") {
+                script "../../../pigz/compress/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ],
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = PIGZ_COMPRESS.out.archive.map { meta, file ->
+                    [[ id: 'test' ], file]
+                }
+                input[1] = MACSYFINDER_DOWNLOAD.out.models
+                input[2] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.best_solutions.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stderr.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stdout.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.summary.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
+    test("macsyfinder_search - proteins - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta', checkIfExists: true)
+                ]
+                input[1] = MACSYFINDER_DOWNLOAD.out.models
+                input[2] = 'TXSScan'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.best_solutions.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stderr.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.stdout.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.summary.collect { meta, filepath -> [ meta, file(filepath).name ] },
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/macsyfinder/search/tests/main.nf.test.snap b/modules/nf-core/macsyfinder/search/tests/main.nf.test.snap
new file mode 100644
index 00000000000..6d6e60ae623
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/tests/main.nf.test.snap
@@ -0,0 +1,153 @@
+{
+    "macsyfinder_search - proteins - fasta": {
+        "content": [
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "macsyfinder.out"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "all_systems.tsv"
+                ]
+            ],
+            {
+                "versions_hmmer": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
+                ],
+                "versions_macsyfinder": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "macsyfinder",
+                        "2.1.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-27T17:00:17.757460737"
+    },
+    "macsyfinder_search - proteins - fasta.gz": {
+        "content": [
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "macsyfinder.out"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "all_systems.tsv"
+                ]
+            ],
+            {
+                "versions_hmmer": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
+                ],
+                "versions_macsyfinder": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "macsyfinder",
+                        "2.1.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-27T17:00:42.224448749"
+    },
+    "macsyfinder_search - proteins - fasta - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "all_best_solutions.txt"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "macsyfinder.err"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "macsyfinder.out"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "all_systems.tsv"
+                ]
+            ],
+            {
+                "versions_hmmer": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "hmmer",
+                        "3.4"
+                    ]
+                ],
+                "versions_macsyfinder": [
+                    [
+                        "MACSYFINDER_SEARCH",
+                        "macsyfinder",
+                        "2.1.6"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-27T17:00:55.062170192"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/macsyfinder/search/tests/nextflow.config b/modules/nf-core/macsyfinder/search/tests/nextflow.config
new file mode 100644
index 00000000000..d805fb7ed47
--- /dev/null
+++ b/modules/nf-core/macsyfinder/search/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: MACSYFINDER_SEARCH {
+        ext.args = '--db-type unordered'
+    }
+}