diff --git a/modules/nf-core/kaiju/mkfmi/main.nf b/modules/nf-core/kaiju/mkfmi/main.nf
index d08be63bb5e..f82c2d75921 100644
--- a/modules/nf-core/kaiju/mkfmi/main.nf
+++ b/modules/nf-core/kaiju/mkfmi/main.nf
@@ -1,18 +1,21 @@
 process KAIJU_MKFMI {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_high'
 
     conda "bioconda::kaiju=1.10.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
-        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0'
+        : 'biocontainers/kaiju:1.10.0--h43eeafb_0'}"
 
     input:
     tuple val(meta), path(fasta)
+    val keep_intermediate
 
     output:
     tuple val(meta), path("*.fmi"), emit: fmi
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.bwt"), optional: true, emit: bwt
+    tuple val(meta), path("*.sa"), optional: true, emit: sa
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,14 +23,17 @@ process KAIJU_MKFMI {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def run_cleanup = keep_intermediate ? "" : "rm -f *.{bwt,sa}"
     """
     kaiju-mkbwt \\
-        $args \\
-        -n $task.cpus \\
+        ${args} \\
+        -n ${task.cpus} \\
         -o ${prefix} \\
         ${fasta}
     kaiju-mkfmi ${prefix}
 
+    ${run_cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
@@ -37,8 +43,13 @@ process KAIJU_MKFMI {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def run_cleanup = keep_intermediate ? "" : "rm -f *.{bwt,sa}"
     """
     touch ${prefix}.fmi
+    touch ${prefix}.bwt
+    touch ${prefix}.sa
+
+    ${run_cleanup}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/kaiju/mkfmi/meta.yml b/modules/nf-core/kaiju/mkfmi/meta.yml
index 16532703735..cb3a5a0aeed 100644
--- a/modules/nf-core/kaiju/mkfmi/meta.yml
+++ b/modules/nf-core/kaiju/mkfmi/meta.yml
@@ -26,6 +26,10 @@ input:
         type: file
         description: Uncompressed Protein FASTA file (mandatory)
         pattern: "*.{fa,faa,fasta}"
+  - - keep_intermediate:
+        type: boolean
+        description: "Keep intermediate files"
+        pattern: true|false
 output:
   - fmi:
       - meta:
@@ -37,6 +41,26 @@ output:
           type: file
           description: Kaiju FM-index file
           pattern: "*.{fmi}"
+  - bwt:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.bwt":
+          type: file
+          description: Kaiju intermedite bwt-index file (not needed for classification)
+          pattern: "*.{bwt}"
+  - sa:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.sa":
+          type: file
+          description: Kaiju intermedite bwt-index file (not needed for classification)
+          pattern: "*.{sa}"
   - versions:
       - versions.yml:
           type: file
@@ -44,3 +68,4 @@ output:
           pattern: "versions.yml"
 authors:
   - "@alxndrdiaz"
+  - "@jfy133"
diff --git a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test
index d8062b0b9f9..68170caeb40 100644
--- a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test
+++ b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test
@@ -18,6 +18,30 @@ nextflow_process {
                         [ id:'test', single_end:true ],
                         file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
                         ]
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - proteome - keep intermediates") {
+
+        when {
+            process {
+                """
+                input[0] =  [
+                        [ id:'test', single_end:true ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                        ]
+                input[1] = true
                 """
             }
         }
@@ -42,6 +66,7 @@ nextflow_process {
                         [ id:'test', single_end:true ],
                         file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
                         ]
+                input[1] = true
                 """
             }
         }
diff --git a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
index 9120a164e4f..8c0ae1b22f1 100644
--- a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
+++ b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
@@ -3,6 +3,10 @@
         "content": [
             "test.fmi"
         ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
         "timestamp": "2024-01-20T16:27:00.670884904"
     },
     "sarscov2 - proteome - fasta": {
@@ -18,7 +22,16 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
                     "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
+                ],
+                "bwt": [
+                    
                 ],
                 "fmi": [
                     [
@@ -29,11 +42,89 @@
                         "test.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
                     ]
                 ],
+                "sa": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-16T09:29:43.118144301"
+    },
+    "sarscov2 - proteome - keep intermediates": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bwt:md5,fe639339371f5b4352017522f54d0c99"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sa:md5,7d4a6481ad5ffdc2058bb35331a64d4d"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
+                ],
+                "bwt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bwt:md5,fe639339371f5b4352017522f54d0c99"
+                    ]
+                ],
+                "fmi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
+                    ]
+                ],
+                "sa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.sa:md5,7d4a6481ad5ffdc2058bb35331a64d4d"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
                 ]
             }
         ],
-        "timestamp": "2024-01-20T16:26:48.062489887"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-16T09:29:47.890853152"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/krakenuniq/build/main.nf b/modules/nf-core/krakenuniq/build/main.nf
index b9a5991a8b2..07c06bebfbe 100644
--- a/modules/nf-core/krakenuniq/build/main.nf
+++ b/modules/nf-core/krakenuniq/build/main.nf
@@ -1,18 +1,19 @@
 process KRAKENUNIQ_BUILD {
-    tag "$meta.id"
+    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/krakenuniq:1.0.4--pl5321h6dccd9a_2':
-        'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.4--pl5321h6dccd9a_2'
+        : 'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2'}"
 
     input:
     tuple val(meta), path(custom_library_dir, stageAs: "library/*"), path(custom_taxonomy_dir, stageAs: "taxonomy"), path(custom_seqid2taxid)
+    val keep_intermediate
 
     output:
-    tuple val(meta), path("$prefix/"), emit: db
-    path "versions.yml"       , emit: versions
+    tuple val(meta), path("${prefix}/"), emit: db
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,15 +21,38 @@ process KRAKENUNIQ_BUILD {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    custom_db     = custom_library_dir ? "mkdir $prefix && mv library taxonomy $custom_seqid2taxid $prefix" : ""
+    custom_db = custom_library_dir ? "mkdir ${prefix} && mv library taxonomy ${custom_seqid2taxid} ${prefix}" : ""
+    run_cleanup = keep_intermediate ? "" : "find -L ${prefix} -type f -not -name \"*.kdb\" -type f -not -name \"*idx\" -not -name \"taxDB\" -delete"
+
     """
-    $custom_db
+    ${custom_db}
 
     krakenuniq-build \\
-        $args \\
+        ${args} \\
         --threads ${task.cpus} \\
         --db ${prefix}
 
+    ${run_cleanup}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    run_cleanup = keep_intermediate ? "" : "find -L ${prefix} -type f -not -name \"*.kdb\" -type f -not -name \"*idx\" -not -name \"taxDB\" -delete"
+    """
+    mkdir ${prefix}/
+    touch ${prefix}/database-build.log
+    touch ${prefix}/database.idx
+    touch ${prefix}/database.jdb
+    touch ${prefix}/database.kdb
+    touch ${prefix}/database.kdb.counts
+    touch ${prefix}/database.kraken.tsv
+    touch ${prefix}/database.report.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
diff --git a/modules/nf-core/krakenuniq/build/meta.yml b/modules/nf-core/krakenuniq/build/meta.yml
index bafc3cfa04e..0322cb68ec1 100644
--- a/modules/nf-core/krakenuniq/build/meta.yml
+++ b/modules/nf-core/krakenuniq/build/meta.yml
@@ -34,6 +34,11 @@ input:
     - custom_seqid2taxid:
         type: file
         description: custom seqid2taxid
+  - - keep_intermediate:
+        type: boolean
+        description: "Keep intermediate files"
+        pattern: true|false
+
 output:
   - db:
       - meta:
@@ -41,7 +46,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - $prefix/:
+      - ${prefix}/:
           type: directory
           description: Directory containing KrakenUniq database
           pattern: "*/"
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test b/modules/nf-core/krakenuniq/build/tests/main.nf.test
new file mode 100644
index 00000000000..c4e77e29846
--- /dev/null
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test
@@ -0,0 +1,126 @@
+nextflow_process {
+
+    name "Test Process KRAKENUNIQ_BUILD"
+    script "../main.nf"
+    process "KRAKENUNIQ_BUILD"
+    config './nextflow.config'
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "krakenuniq"
+    tag "krakenuniq/build"
+    tag "krakenuniq/download"
+
+    setup {
+        run("KRAKENUNIQ_DOWNLOAD"){
+            script "../../download/main.nf"
+            process {
+            """
+            input[0] = 'taxonomy'
+            """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                ch_fastas      = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ch_seqid2mapid = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true)
+
+                ch_input = ch_fastas
+                            .combine(KRAKENUNIQ_DOWNLOAD.out.output)
+                            .combine(ch_seqid2mapid)
+                            .map {
+                                fna, tax, map ->
+
+                                [ [id:'test'] , fna, tax, map ]
+                            }
+
+                input[0] = ch_input
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            def stablefiles = []
+            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
+            def unstablefiles = []
+            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        stablefiles.sort(),
+                        unstablefiles.sort(),
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+test("sarscov2 - fasta - nocleanup") {
+
+        when {
+            process {
+                """
+                ch_fastas      = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ch_seqid2mapid = Channel.fromPath(params.modules_testdata_base_path + 'genomics/sarscov2/metagenome/seqid2taxid.map', checkIfExists: true)
+
+                ch_input = ch_fastas
+                            .combine(KRAKENUNIQ_DOWNLOAD.out.output)
+                            .combine(ch_seqid2mapid)
+                            .map {
+                                fna, tax, map ->
+
+                                [ [id:'test'] , fna, tax, map ]
+                            }
+
+                input[0] = ch_input
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            def stablefiles = []
+            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (!file.isDirectory() && !["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
+            def unstablefiles = []
+            file(process.out.db.get(0).get(1)).eachFileRecurse{ file -> if (["database-build.log", "database.report.tsv", "timestamp", "taxdump.tar.gz", "names.dmp", "nodes.dmp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        stablefiles.sort(),
+                        unstablefiles.sort(),
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [[id:'test'], [] , [] , []]
+                input[1] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                )
+        }
+    }
+}
diff --git a/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
new file mode 100644
index 00000000000..fb3f1327e16
--- /dev/null
+++ b/modules/nf-core/krakenuniq/build/tests/main.nf.test.snap
@@ -0,0 +1,104 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "database-build.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.jdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kdb.counts:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kraken.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "database-build.log:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.idx:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.jdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kdb.counts:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.kraken.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "database.report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-16T14:19:28.193479362"
+    },
+    "sarscov2 - fasta - nocleanup": {
+        "content": [
+            [
+                "database.idx:md5,f5298aa4215c956d2f737b5988721a24",
+                "database.jdb:md5,48db5f6bb9b9e9db7f5bbdd0d8bec4a8",
+                "database.kdb:md5,46542be19979e867075f9e455a314e00",
+                "database.kdb.counts:md5,a82149480a435210ec1e870f06b6cdb3",
+                "database.kraken.tsv:md5,be9bd0cb3a8bea30989e65aa42a73727",
+                "database0.kdb:md5,46542be19979e867075f9e455a314e00",
+                "library-files.txt:md5,8a9817d2de8465eb436aa3aa8696a717",
+                "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
+                "seqid2taxid.map:md5,fe738f2333d57dde0db32239c04a93b8",
+                "taxDB:md5,37ea954363803b13c2c9f6ae36fc81c7"
+            ],
+            [
+                "database-build.log",
+                "database.report.tsv",
+                "names.dmp",
+                "nodes.dmp",
+                "taxdump.tar.gz",
+                "timestamp"
+            ],
+            [
+                "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-17T08:29:04.791324194"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            [
+                "database.idx:md5,f5298aa4215c956d2f737b5988721a24",
+                "database.kdb:md5,46542be19979e867075f9e455a314e00",
+                "database0.kdb:md5,46542be19979e867075f9e455a314e00",
+                "taxDB:md5,37ea954363803b13c2c9f6ae36fc81c7"
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,b7fb6c70957b2e6b6b810757928d0325"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-17T08:28:18.051752599"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/krakenuniq/build/tests/nextflow.config b/modules/nf-core/krakenuniq/build/tests/nextflow.config
new file mode 100644
index 00000000000..11e267e03c6
--- /dev/null
+++ b/modules/nf-core/krakenuniq/build/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: KRAKENUNIQ_BUILD {
+        ext.args = "--work-on-disk --max-db-size 12 --kmer-len 15 --minimizer-len 13 --jellyfish-bin \"\$(which jellyfish)\""
+    }
+}
diff --git a/modules/nf-core/krakenuniq/download/main.nf b/modules/nf-core/krakenuniq/download/main.nf
index 8ef3eff2b90..abfa89961f4 100644
--- a/modules/nf-core/krakenuniq/download/main.nf
+++ b/modules/nf-core/krakenuniq/download/main.nf
@@ -2,16 +2,16 @@ process KRAKENUNIQ_DOWNLOAD {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.4--pl5321h6dccd9a_2':
-        'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/krakenuniq:1.0.4--pl5321h6dccd9a_2'
+        : 'biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_2'}"
 
     input:
     val pattern
 
     output:
-    path "${pattern}/"  , emit: output
-    path "versions.yml" , emit: versions
+    path "${pattern}/", emit: output
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,7 +23,18 @@ process KRAKENUNIQ_DOWNLOAD {
         --threads ${task.cpus} \\
         -o ${pattern}/ \\
         ${pattern} \\
-        $args
+        ${args}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krakenuniq: \$(echo \$(krakenuniq --version 2>&1) | sed 's/^.*KrakenUniq version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    mkdir ${pattern}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/krakenuniq/download/tests/main.nf.test b/modules/nf-core/krakenuniq/download/tests/main.nf.test
new file mode 100644
index 00000000000..edef7bfea3b
--- /dev/null
+++ b/modules/nf-core/krakenuniq/download/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process KRAKENUNIQ_DOWNLOAD"
+    script "../main.nf"
+    process "KRAKENUNIQ_DOWNLOAD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "krakenuniq"
+    tag "krakenuniq/download"
+    tag "debug"
+
+    test("taxonomy") {
+
+        when {
+            process {
+                """
+                input[0] = 'taxonomy'
+                """
+            }
+        }
+
+        then {
+            println('HHELLLOOOOO')
+            def stablefiles = []
+            file(process.out.output.get(0)).eachFileRecurse{ file -> if (!file.isDirectory() && !["timestamp"].find {file.toString().endsWith(it)}) {stablefiles.add(file)} }
+            println(stablefiles)
+            def unstablefiles = []
+            file(process.out.output.get(0)).eachFileRecurse{ file -> if (["timestamp"].find {file.toString().endsWith(it)}) {unstablefiles.add(file.getName().toString())} }
+            println(unstablefiles)
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        stablefiles.sort(),
+                        unstablefiles.sort(),
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("taxonomy - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = 'taxonomy'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap b/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bdea7d86ea6
--- /dev/null
+++ b/modules/nf-core/krakenuniq/download/tests/main.nf.test.snap
@@ -0,0 +1,49 @@
+{
+    "taxonomy - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09"
+                ],
+                "output": [
+                    [
+                        
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-17T08:39:20.362801897"
+    },
+    "taxonomy": {
+        "content": [
+            [
+                "names.dmp:md5,aae05a99d67ea8a593f8642b40e98f28",
+                "nodes.dmp:md5,73f515a0c4be7a324a6717bbe14cd274",
+                "taxdump.tar.gz:md5,4ec3d4430ef2d350db5b3284edd33a8b"
+            ],
+            [
+                "timestamp"
+            ],
+            [
+                "versions.yml:md5,a12e821f0d977f77c0c905a89c708d09"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-01-17T09:01:52.533204202"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 6eef66aaa8b..f8edf0986e5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -266,12 +266,6 @@ kofamscan:
 krakentools/combinekreports:
   - modules/nf-core/krakentools/combinekreports/**
   - tests/modules/nf-core/krakentools/combinekreports/**
-krakenuniq/build:
-  - modules/nf-core/krakenuniq/build/**
-  - tests/modules/nf-core/krakenuniq/build/**
-krakenuniq/download:
-  - modules/nf-core/krakenuniq/download/**
-  - tests/modules/nf-core/krakenuniq/download/**
 krona/kronadb:
   - modules/nf-core/krona/kronadb/**
   - tests/modules/nf-core/krona/kronadb/**
diff --git a/tests/modules/nf-core/krakenuniq/build/main.nf b/tests/modules/nf-core/krakenuniq/build/main.nf
deleted file mode 100644
index 63fba4866cb..00000000000
--- a/tests/modules/nf-core/krakenuniq/build/main.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRAKENUNIQ_DOWNLOAD } from '../../../../../modules/nf-core/krakenuniq/download/main.nf'
-include { KRAKENUNIQ_BUILD    } from '../../../../../modules/nf-core/krakenuniq/build/main.nf'
-
-workflow test_krakenuniq_build {
-
-    ch_fastas      = Channel.fromPath(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ch_seqid2mapid = Channel.fromPath(params.test_data['sarscov2']['metagenome']['seqid2taxid_map'], checkIfExists: true)
-    KRAKENUNIQ_DOWNLOAD ( 'taxonomy' )
-
-    ch_input = ch_fastas
-                    .combine(KRAKENUNIQ_DOWNLOAD.out.output)
-                    .combine(ch_seqid2mapid)
-                    .map {
-                        fna, tax, map ->
-
-                        [ [id: "customdb"], fna, tax, map ]
-                    }
-
-    KRAKENUNIQ_BUILD ( ch_input )
-}
diff --git a/tests/modules/nf-core/krakenuniq/build/nextflow.config b/tests/modules/nf-core/krakenuniq/build/nextflow.config
deleted file mode 100644
index 113299318e5..00000000000
--- a/tests/modules/nf-core/krakenuniq/build/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: 'KRAKENUNIQ_BUILD' {
-        ext.args ="--work-on-disk"
-    }
-
-}
diff --git a/tests/modules/nf-core/krakenuniq/build/test.yml b/tests/modules/nf-core/krakenuniq/build/test.yml
deleted file mode 100644
index f36f385f174..00000000000
--- a/tests/modules/nf-core/krakenuniq/build/test.yml
+++ /dev/null
@@ -1,30 +0,0 @@
-- name: krakenuniq build test_krakenuniq_build
-  command: nextflow run ./tests/modules/nf-core/krakenuniq/build -entry test_krakenuniq_build -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/krakenuniq/build/nextflow.config
-  tags:
-    - krakenuniq/build
-    - krakenuniq
-  files:
-    - path: output/krakenuniq/customdb/database-build.log
-      contains: ["-d database.jdb -o database0.kdb.tmp -i database.idx"]
-    - path: output/krakenuniq/customdb/database.idx
-      md5sum: db9e8cd1f75cdedd70dd346b70658790
-    - path: output/krakenuniq/customdb/database.jdb
-      md5sum: 8b4a9b8cbcacec61fc6a220f0cec59bd
-    - path: output/krakenuniq/customdb/database.kdb
-      md5sum: c6853c5d2f3a4a7ad05c2973a993b9b8
-    - path: output/krakenuniq/customdb/database.kdb.counts
-      md5sum: a82149480a435210ec1e870f06b6cdb3
-    - path: output/krakenuniq/customdb/database.kraken.tsv
-      md5sum: 8aafacd89a6aac98aaf512df0a7493d1
-    - path: output/krakenuniq/customdb/database.report.tsv
-      contains: ["%       reads   taxReads        kmers   dup     cov     taxID   rank    taxName"]
-    - path: output/krakenuniq/customdb/database0.kdb
-      md5sum: c6853c5d2f3a4a7ad05c2973a993b9b8
-    - path: output/krakenuniq/customdb/library-files.txt
-      md5sum: 8a9817d2de8465eb436aa3aa8696a717
-    - path: output/krakenuniq/customdb/library/genome.fasta
-      md5sum: 6e9fe4042a72f2345f644f239272b7e6
-    - path: output/krakenuniq/customdb/seqid2taxid.map
-      md5sum: fe738f2333d57dde0db32239c04a93b8
-    - path: output/krakenuniq/customdb/taxDB
-      md5sum: 84213970a13958e612a0eb0f4681fbc4
diff --git a/tests/modules/nf-core/krakenuniq/download/main.nf b/tests/modules/nf-core/krakenuniq/download/main.nf
deleted file mode 100644
index 418561dc320..00000000000
--- a/tests/modules/nf-core/krakenuniq/download/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRAKENUNIQ_DOWNLOAD } from '../../../../../modules/nf-core/krakenuniq/download/main.nf'
-
-workflow test_krakenuniq_download {
-
-    input = "taxonomy"
-
-    KRAKENUNIQ_DOWNLOAD ( input )
-}
diff --git a/tests/modules/nf-core/krakenuniq/download/nextflow.config b/tests/modules/nf-core/krakenuniq/download/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/krakenuniq/download/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/krakenuniq/download/test.yml b/tests/modules/nf-core/krakenuniq/download/test.yml
deleted file mode 100644
index 63fdcfc4cae..00000000000
--- a/tests/modules/nf-core/krakenuniq/download/test.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-- name: krakenuniq download test_krakenuniq_download
-  command: nextflow run ./tests/modules/nf-core/krakenuniq/download -entry test_krakenuniq_download -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/krakenuniq/download/nextflow.config
-  tags:
-    - krakenuniq
-    - krakenuniq/download
-  files:
-    - path: output/krakenuniq/taxonomy/names.dmp
-      contains: ["scientific name"]
-    - path: output/krakenuniq/taxonomy/nodes.dmp
-      contains: ["superkingdom"]
-    - path: output/krakenuniq/taxonomy/taxdump.tar.gz
-    - path: output/krakenuniq/taxonomy/timestamp