diff --git a/CITATIONS.md b/CITATIONS.md
index 5b5379a..8451b47 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -52,6 +52,10 @@
 
 > Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257. https://doi.org/10.1038/ncomms11257
 
+- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
+
+  > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0
+
 - [MALT](https://doi.org/10.1038/s41559-017-0446-6)
 
   > Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528. https://doi.org/10.1038/s41559-017-0446-6
diff --git a/README.md b/README.md
index 034055e..4ab60ec 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@
 
 ## Introduction
 
-**nf-core/createtaxdb** is a bioinformatics pipeline that constructs metagenomic classifier databases from the same input reference genome set for multiple classifiers and profilers in a highly automated and parallelised manner.
+**nf-core/createtaxdb** is a bioinformatics pipeline that constructs custom metagenomic classifier databases from the same input reference genome set for multiple classifiers and profilers in a highly automated and parallelised manner.
 
 <!-- TODO nf-core:
    Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
@@ -35,6 +35,7 @@
    - [Centrifuge](https://doi.org/10.1101/gr.210641.116)
    - [DIAMOND](https://doi.org/10.1038/nmeth.3176)
    - [Kaiju](https://doi.org/10.1038/ncomms11257)
+   - [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
    - [MALT](https://doi.org/10.1038/s41559-017-0446-6)
 
 ## Usage
diff --git a/conf/modules.config b/conf/modules.config
index 4fd237e..a2ff3f1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -57,7 +57,6 @@ process {
 
     withName: 'MALT_BUILD' {
         ext.args   = { "--sequenceType ${params.malt_sequencetype}" }
-
     }
 
 }
diff --git a/conf/test.config b/conf/test.config
index a2a13e1..371fe8b 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -27,7 +27,9 @@ params {
     build_kaiju      = true
     build_malt       = true
     build_centrifuge = true
+    build_kraken2    = true
 
+    accession2taxid  = 'https://raw.githubusercontent.com/nf-core/test-datasets/createtaxdb/data/taxonomy/nucl_gb.accession2taxid'
     nucl2taxid       = 'https://raw.githubusercontent.com/nf-core/test-datasets/createtaxdb/data/taxonomy/nucl2tax.map'
     prot2taxid       = 'https://raw.githubusercontent.com/nf-core/test-datasets/createtaxdb/data/taxonomy/prot.accession2taxid.gz'
     nodesdmp         = 'https://raw.githubusercontent.com/nf-core/test-datasets/createtaxdb/data/taxonomy/nodes.dmp'
diff --git a/conf/test_nothing.config b/conf/test_nothing.config
index 17ae64a..72c07e3 100644
--- a/conf/test_nothing.config
+++ b/conf/test_nothing.config
@@ -29,5 +29,6 @@ params {
     build_kaiju      = false
     build_malt       = false
     build_centrifuge = false
+    build_kraken2    = false
 
 }
diff --git a/docs/output.md b/docs/output.md
index 1246ace..5a54002 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -17,6 +17,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Centrifuge](#centrifuge) - Database files for Centrifuge
 - [DIAMOND](#diamond) - Database files for DIAMOND
 - [Kaiju](#kaiju) - Database files for Kaiju
+- [Kraken2](#kraken2) - Database files for Kraken2
 - [MALT](#malt) - Database files for MALT
 
 ### MultiQC
@@ -92,6 +93,23 @@ The `dmnd` file can be given to one of the DIAMOND alignment commands with `diam
 
 The `fmi` file can be given to Kaiju itself with `kaiju -f <your_database>.fmi` etc.
 
+### Kraken2
+
+[Kraken2](https://ccb.jhu.edu/software/kraken2/) is a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `kraken2/`
+  - `<db_name>/`
+    - `hash.k2d`: Kraken2 hash database file
+    - `opts.k2d`: Kraken2 opts database file
+    - `taxo.k2d`: Kraken2 taxo database file
+
+</details>
+
+The resulting `<db_name>/` directory can be given to Kraken2 itself with `kraken2 --db <your_database_name>` etc.
+
 ### MALT
 
 [MALT](https://software-ab.cs.uni-tuebingen.de/download/malt) is a fast replacement for BLASTX, BLASTP and BLASTN, and provides both local and semi-global alignment capabilities.
diff --git a/main.nf b/main.nf
index 5214b78..451a6c5 100644
--- a/main.nf
+++ b/main.nf
@@ -40,8 +40,24 @@ workflow NFCORE_CREATETAXDB {
     //
     // WORKFLOW: Run pipeline
     //
+    ch_samplesheet       = samplesheet
+    ch_taxonomy_namesdmp = file(params.namesdmp)
+    ch_taxonomy_nodesdmp = file(params.nodesdmp)
+    ch_accession2taxid   = file(params.accession2taxid)
+    ch_nucl2taxid        = file(params.nucl2taxid)
+    ch_prot2taxid        = file(params.prot2taxid)
+    ch_malt_mapdb        = file(params.malt_mapdb)
+
+
     CREATETAXDB (
-        samplesheet
+        ch_samplesheet,
+        ch_taxonomy_namesdmp,
+        ch_taxonomy_nodesdmp,
+        ch_accession2taxid,
+        ch_nucl2taxid,
+        ch_prot2taxid,
+        ch_malt_mapdb,
+
     )
 
     emit:
diff --git a/modules.json b/modules.json
index 7082ace..cb08493 100644
--- a/modules.json
+++ b/modules.json
@@ -25,11 +25,26 @@
                         "git_sha": "b29f6beb86d1d24d680277fb1a3f4de7b8b8a92c",
                         "installed_by": ["modules"]
                     },
+                    "gunzip": {
+                        "branch": "master",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
+                        "installed_by": ["modules"]
+                    },
                     "kaiju/mkfmi": {
                         "branch": "master",
                         "git_sha": "7365564c402cbd01e9407810730efd10039997a3",
                         "installed_by": ["modules"]
                     },
+                    "kraken2/add": {
+                        "branch": "master",
+                        "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2",
+                        "installed_by": ["fasta_build_add_kraken2"]
+                    },
+                    "kraken2/build": {
+                        "branch": "master",
+                        "git_sha": "ca87ad032a62f025f0c373facacef2df0c5411b2",
+                        "installed_by": ["fasta_build_add_kraken2"]
+                    },
                     "malt/build": {
                         "branch": "master",
                         "git_sha": "7d3bac628092d1aead36960c4b6ae41302a9f797",
@@ -54,6 +69,11 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "fasta_build_add_kraken2": {
+                        "branch": "master",
+                        "git_sha": "a4d1e13a2da05307deb65a87d501aa6520162dcd",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
new file mode 100644
index 0000000..25910b3
--- /dev/null
+++ b/modules/nf-core/gunzip/environment.yml
@@ -0,0 +1,7 @@
+name: gunzip
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
new file mode 100644
index 0000000..468a6f2
--- /dev/null
+++ b/modules/nf-core/gunzip/main.nf
@@ -0,0 +1,48 @@
+process GUNZIP {
+    tag "$archive"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(archive)
+
+    output:
+    tuple val(meta), path("$gunzip"), emit: gunzip
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    gunzip = archive.toString() - '.gz'
+    """
+    # Not calling gunzip itself because it creates files
+    # with the original group ownership rather than the
+    # default one for that user / the work directory
+    gzip \\
+        -cd \\
+        $args \\
+        $archive \\
+        > $gunzip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    gunzip = archive.toString() - '.gz'
+    """
+    touch $gunzip
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
new file mode 100644
index 0000000..231034f
--- /dev/null
+++ b/modules/nf-core/gunzip/meta.yml
@@ -0,0 +1,39 @@
+name: gunzip
+description: Compresses and decompresses files.
+keywords:
+  - gunzip
+  - compression
+  - decompression
+tools:
+  - gunzip:
+      description: |
+        gzip is a file format and a software application used for file compression and decompression.
+      documentation: https://www.gnu.org/software/gzip/manual/gzip.html
+      licence: ["GPL-3.0-or-later"]
+input:
+  - meta:
+      type: map
+      description: |
+        Optional groovy Map containing meta information
+        e.g. [ id:'test', single_end:false ]
+  - archive:
+      type: file
+      description: File to be compressed/uncompressed
+      pattern: "*.*"
+output:
+  - gunzip:
+      type: file
+      description: Compressed/uncompressed file
+      pattern: "*.*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
new file mode 100644
index 0000000..6406008
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process GUNZIP"
+    script "../main.nf"
+    process "GUNZIP"
+    tag "gunzip"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                        [],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
new file mode 100644
index 0000000..720fd9f
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ],
+                "gunzip": [
+                    [
+                        [
+                            
+                        ],
+                        "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-17T15:35:37.690477896"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml
new file mode 100644
index 0000000..fd3f691
--- /dev/null
+++ b/modules/nf-core/gunzip/tests/tags.yml
@@ -0,0 +1,2 @@
+gunzip:
+  - modules/nf-core/gunzip/**
diff --git a/modules/nf-core/kraken2/add/environment.yml b/modules/nf-core/kraken2/add/environment.yml
new file mode 100644
index 0000000..24b1c0e
--- /dev/null
+++ b/modules/nf-core/kraken2/add/environment.yml
@@ -0,0 +1,11 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "kraken2_add"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::kraken2=2.1.3"
+  - "coreutils=9.4"
+  - "pigz=2.8"
diff --git a/modules/nf-core/kraken2/add/main.nf b/modules/nf-core/kraken2/add/main.nf
new file mode 100644
index 0000000..36d3abb
--- /dev/null
+++ b/modules/nf-core/kraken2/add/main.nf
@@ -0,0 +1,56 @@
+process KRAKEN2_ADD {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' :
+        'biocontainers/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path taxonomy_names, stageAs: 'taxonomy/names.dmp'
+    path taxonomy_nodes, stageAs: 'taxonomy/nodes.dmp'
+    path accession2taxid, stageAs: 'taxonomy/*'
+
+    output:
+    tuple val(meta), path("$prefix"), emit: db
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    mv "taxonomy" ${prefix}
+
+    echo ${fasta} |\\
+    tr -s " " "\\012" |\\
+    xargs -I {} -n1 kraken2-build \\
+        --add-to-library {} \\
+        --db ${prefix} \\
+        --threads $task.cpus \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir "$prefix"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/kraken2/add/meta.yml b/modules/nf-core/kraken2/add/meta.yml
new file mode 100644
index 0000000..e5bc2d7
--- /dev/null
+++ b/modules/nf-core/kraken2/add/meta.yml
@@ -0,0 +1,57 @@
+name: kraken2_add
+description: Adds fasta files to a Kraken2 taxonomic database
+keywords:
+  - metagenomics
+  - db
+  - classification
+  - build
+  - kraken2
+  - add
+tools:
+  - kraken2:
+      description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies."
+      homepage: https://ccb.jhu.edu/software/kraken2/
+      documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
+      tool_dev_url: "https://github.com/DerrickWood/kraken2"
+      doi: 10.1186/s13059-019-1891-0
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - fasta:
+      type: file
+      description: fasta file that will be added to the database
+      pattern: "*.{fa,fasta,fna,ffn}"
+  - taxonomy_names:
+      type: file
+      description: used for associating sequences with taxonomy IDs
+      pattern: "*.dmp"
+  - taxonomy_nodes:
+      type: file
+      description: tree nodes using NCBI taxonomy nomenclature
+      pattern: "*.dmp"
+  - accession2taxid:
+      type: file
+      description: associates sequence accession IDs to taxonomy IDs
+      pattern: "*.accession2taxid"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - db:
+      type: directory
+      description: contains required files to build the database
+      pattern: "*/"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@alxndrdiaz"
+maintainers:
+  - "@alxndrdiaz"
diff --git a/modules/nf-core/kraken2/add/tests/main.nf.test b/modules/nf-core/kraken2/add/tests/main.nf.test
new file mode 100644
index 0000000..322f4e3
--- /dev/null
+++ b/modules/nf-core/kraken2/add/tests/main.nf.test
@@ -0,0 +1,92 @@
+nextflow_process {
+
+    name "Test Process KRAKEN2_ADD"
+    script "../main.nf"
+    process "KRAKEN2_ADD"
+    tag "kraken2"
+    tag "kraken2/add"
+    tag "gunzip"
+    tag "modules"
+    tag "modules_nfcore"
+
+    setup {
+        run("GUNZIP") {
+            script "modules/nf-core/gunzip/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [],
+                    file(
+                        params.test_data['sarscov2']['metagenome']['prot_accession2taxid_gz'],
+                        checkIfExists: true
+                    )
+                ])
+                """
+            }
+        }
+    }
+
+    test("sarscov2 protein_db") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                        [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                        ]
+                    ]
+                input[1] = file(params.test_data['sarscov2']['metagenome']['prot_names_dmp'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['metagenome']['prot_nodes_dmp'], checkIfExists: true)
+                input[3] = GUNZIP.out.gunzip.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.db.get(0).get(1) ==~ ".*/test" },
+                { assert snapshot (
+                        path("${process.out.db[0][1]}/library/added/").list().size(),
+                        path("${process.out.db[0][1]}/taxonomy/")
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+test("sarscov2 protein_db stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                        [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                        ]
+                    ]
+                input[1] = file(params.test_data['sarscov2']['metagenome']['prot_names_dmp'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['metagenome']['prot_nodes_dmp'], checkIfExists: true)
+                input[3] = GUNZIP.out.gunzip.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot (process.out).match()
+                }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/kraken2/add/tests/main.nf.test.snap b/modules/nf-core/kraken2/add/tests/main.nf.test.snap
new file mode 100644
index 0000000..5050d69
--- /dev/null
+++ b/modules/nf-core/kraken2/add/tests/main.nf.test.snap
@@ -0,0 +1,54 @@
+{
+    "sarscov2 protein_db": {
+        "content": [
+            6,
+            [
+                "names.dmp:md5,130f9132095562e09c732679c562f5e9",
+                "nodes.dmp:md5,c471c27a4ce85ae74d2c63633c9ce1e3",
+                "prot.accession2taxid:md5,c0f96ba5dbb00150b4b805ba6dab7bea"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T20:20:05.09765"
+    },
+    "sarscov2 protein_db stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9a7b40921622d8c873fb3bfd8bac4c3d"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9a7b40921622d8c873fb3bfd8bac4c3d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-20T09:07:41.484004342"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kraken2/add/tests/tags.yml b/modules/nf-core/kraken2/add/tests/tags.yml
new file mode 100644
index 0000000..3ee6390
--- /dev/null
+++ b/modules/nf-core/kraken2/add/tests/tags.yml
@@ -0,0 +1,3 @@
+kraken2/add:
+  - modules/nf-core/kraken2/add/**
+  - modules/nf-core/gunzip/**
diff --git a/modules/nf-core/kraken2/build/environment.yml b/modules/nf-core/kraken2/build/environment.yml
new file mode 100644
index 0000000..5624c5e
--- /dev/null
+++ b/modules/nf-core/kraken2/build/environment.yml
@@ -0,0 +1,11 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "kraken2_build"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::kraken2=2.1.3"
+  - "coreutils=9.4"
+  - "pigz=2.8"
diff --git a/modules/nf-core/kraken2/build/main.nf b/modules/nf-core/kraken2/build/main.nf
new file mode 100644
index 0000000..caba65f
--- /dev/null
+++ b/modules/nf-core/kraken2/build/main.nf
@@ -0,0 +1,51 @@
+process KRAKEN2_BUILD {
+    tag "$meta.id"
+    label 'process_medium'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0':
+        'biocontainers/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' }"
+
+    input:
+    tuple val(meta), path(db)
+    val cleaning
+
+    output:
+    tuple val(meta), path("$prefix"), emit: db
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    runclean = cleaning ? "kraken2-build --clean --db ${db}" : ""
+    """
+    kraken2-build \\
+        --build \\
+        $args \\
+        --threads ${task.cpus} \\
+        --db ${db}
+    $runclean
+    if [[ \$(basename ${db}) != "${prefix}" ]]; then
+        mv ${db}/* ${prefix}
+    fi
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p "$prefix"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml
new file mode 100644
index 0000000..50f6d19
--- /dev/null
+++ b/modules/nf-core/kraken2/build/meta.yml
@@ -0,0 +1,48 @@
+name: "kraken2_build"
+description: Builds Kraken2 database
+keywords:
+  - metagenomics
+  - db
+  - classification
+  - build
+  - kraken2
+tools:
+  - kraken2:
+      description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies."
+      homepage: https://ccb.jhu.edu/software/kraken2/
+      documentation: https://github.com/DerrickWood/kraken2/wiki/Manual
+      tool_dev_url: "https://github.com/DerrickWood/kraken2"
+      doi: 10.1186/s13059-019-1891-0
+      licence: ["MIT"]
+      args_id: "$args"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - db:
+      type: directory
+      description: contains required files to build the database
+      pattern: "*/"
+  - cleaning:
+      type: boolean
+      description: activate or deactivate (true or false) cleaning of intermediate files
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - db:
+      type: directory
+      description: contains the database that can be used to perform taxonomic classification
+      pattern: "*/"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@alxndrdiaz"
+maintainers:
+  - "@alxndrdiaz"
diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test b/modules/nf-core/kraken2/build/tests/main.nf.test
new file mode 100644
index 0000000..9eec2cc
--- /dev/null
+++ b/modules/nf-core/kraken2/build/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process KRAKEN2_BUILD"
+    script "../main.nf"
+    process "KRAKEN2_BUILD"
+    config "./nextflow.config"
+    tag "kraken2"
+    tag "kraken2/build"
+    tag "kraken2/add"
+    tag "gunzip"
+    tag "modules"
+    tag "modules_nfcore"
+
+    setup {
+
+        run("GUNZIP") {
+            script "modules/nf-core/gunzip/main.nf"
+            process {
+                """
+                input[0] = Channel.of([
+                    [],
+                    file(
+                        params.test_data['sarscov2']['metagenome']['prot_accession2taxid_gz'],
+                        checkIfExists: true
+                    )
+                ])
+                """
+            }
+        }
+
+        run("KRAKEN2_ADD") {
+            script "modules/nf-core/kraken2/add/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                        [
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
+                        ]
+                    ]
+                input[1] = file(params.test_data['sarscov2']['metagenome']['prot_names_dmp'], checkIfExists: true)
+                input[2] = file(params.test_data['sarscov2']['metagenome']['prot_nodes_dmp'], checkIfExists: true)
+                input[3] = GUNZIP.out.gunzip.map{ it[1] }
+                """
+            }
+        }
+
+    }
+
+    test("sarscov2 protein_db") {
+
+        when {
+            process {
+                """
+                input[0] = KRAKEN2_ADD.out.db
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.db.get(0).get(1) ==~ ".*/test" },
+                { assert snapshot (
+                        path("${process.out.db[0][1]}/hash.k2d"),
+                        path("${process.out.db[0][1]}/taxo.k2d"),
+                        file("${process.out.db[0][1]}/opts.k2d").name,
+                        file("${process.out.db[0][1]}/unmapped.txt").name
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("sarscov2 protein_db stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = KRAKEN2_ADD.out.db
+                input[1] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot (process.out).match()
+                }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/kraken2/build/tests/main.nf.test.snap b/modules/nf-core/kraken2/build/tests/main.nf.test.snap
new file mode 100644
index 0000000..fb87c51
--- /dev/null
+++ b/modules/nf-core/kraken2/build/tests/main.nf.test.snap
@@ -0,0 +1,52 @@
+{
+    "sarscov2 protein_db": {
+        "content": [
+            "hash.k2d:md5,e9984a5e98f87c0488cb5e7618d5bbe0",
+            "taxo.k2d:md5,29d65b1796e09191fd7bdcaa24130459",
+            "opts.k2d",
+            "unmapped.txt"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-22T08:10:48.644001909"
+    },
+    "sarscov2 protein_db stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,df044948ec1fdb342a1d6fadde84b334"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,df044948ec1fdb342a1d6fadde84b334"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T17:41:57.715748"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kraken2/build/tests/nextflow.config b/modules/nf-core/kraken2/build/tests/nextflow.config
new file mode 100644
index 0000000..11ac39e
--- /dev/null
+++ b/modules/nf-core/kraken2/build/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: KRAKEN2_BUILD {
+        ext.args = '--protein'
+    }
+
+}
diff --git a/modules/nf-core/kraken2/build/tests/tags.yml b/modules/nf-core/kraken2/build/tests/tags.yml
new file mode 100644
index 0000000..4a5e61d
--- /dev/null
+++ b/modules/nf-core/kraken2/build/tests/tags.yml
@@ -0,0 +1,4 @@
+kraken2/build:
+  - modules/nf-core/kraken2/build/**
+  - modules/nf-core/kraken2/add/**
+  - modules/nf-core/gunzip/**
diff --git a/nextflow.config b/nextflow.config
index 231478b..4725942 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -56,18 +56,21 @@ params {
     dbname                   = "database"
     save_concatenated_fastas = false
 
-    prot2taxid = null
-    nucl2taxid  = null
-    nodesdmp   = null
-    namesdmp   = null
-    malt_mapdb = null
+    accession2taxid = null
+    prot2taxid      = null
+    nucl2taxid      = null
+    nodesdmp        = null
+    namesdmp        = null
+    malt_mapdb      = null
 
     // tool specific options
-    build_diamond     = false
-    build_kaiju       = false
-    build_malt        = false
-    malt_sequencetype = "DNA"
-    build_centrifuge  = false
+    build_diamond            = false
+    build_kaiju              = false
+    build_malt               = false
+    malt_sequencetype        = "DNA"
+    build_centrifuge         = false
+    build_kraken2            = false
+    kraken2_keepintermediate = false
 
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 04898fb..b1344ea 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -47,20 +47,27 @@
                     "description": "Specify name that resulting databases will be prefixed with.",
                     "fa_icon": "fas fa-id-badge"
                 },
+                "accession2taxid": {
+                    "type": "string",
+                    "description": "NCBI-style four-column accession to taxonomy ID map file",
+                    "help_text": "\nAn NCBI four column file tab-separated file with `accession`, `accession.version`, `taxid` and `gi` number. The first refers to an accession ID in each FASTA entry header. The second refers to the accession ID but with the accession version number appended to the end (e.g. `.1`). The third refers to the taxonomy ID of the organism the sequence belongs to, as listed in `nodes.dmp`. The fourth refers to the old-style NCBI gi number of the sequence.\n\nIf building with typical NCBI data, the most typical file is the `nucl_gb.accession2taxid` file from the [NCBI taxonomy FTP server](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/.",
+                    "fa_icon": "fas fa-address-book",
+                    "format": "file-path"
+                },
                 "prot2taxid": {
                     "type": "string",
-                    "format": "file-path",
+                    "format": "path",
                     "exists": true,
                     "fa_icon": "fas fa-address-card",
-                    "description": "Path to (NCBI-style) protein accession2taxid file.",
-                    "help_text": "A two column file tab-separated file with `accession.version` and `taxid`. The first refers to an accession ID in each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in `nodes.dmp`."
+                    "help_text": "A two column file tab-separated file with `accession.version` and `taxid`. The first refers to an accession ID in each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in `nodes.dmp`.",
+                    "description": "Two column protein sequence accession ID to taxonomy map file."
                 },
                 "nucl2taxid": {
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
                     "fa_icon": "far fa-address-card",
-                    "description": "Path to (NCBI-style) nucleotide accession2taxid file.",
+                    "description": "Two column nucleotide sequence accession ID to taxonomy map file.",
                     "help_text": "A two column file tab-separated file with `accession.version` and `taxid`. The first refers to an accession ID in each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in `nodes.dmp`."
                 },
                 "nodesdmp": {
@@ -90,7 +97,8 @@
                 "save_concatenated_fastas": {
                     "type": "boolean",
                     "description": "Save concatenated input FASTAs",
-                    "help_text": "Some tools require a single input FASTA of all reference genomes. The pipeline will do this concatenation for you, and by supplying this flag you can save the resulting single fasta for you in the results directory under `cat/`. "
+                    "help_text": "Some tools require a single input FASTA of all reference genomes. The pipeline will do this concatenation for you, and by supplying this flag you can save the resulting single fasta for you in the results directory under `cat/`. ",
+                    "fa_icon": "fas fa-save"
                 }
             }
         },
@@ -127,6 +135,16 @@
                     "enum": ["DNA", "Protein"],
                     "help_text": "Use to specify whether the reference sequences are DNA or Protein sequences. (For RNA sequences, use the DNA setting) - from [MALT manual](https://software-ab.cs.uni-tuebingen.de/download/malt/).\n\n> Modifies tool(s) parameter(s)\n> - malt-build: `--sequenceType` ",
                     "fa_icon": "fas fa-dna"
+                },
+                "build_kraken2": {
+                    "type": "boolean",
+                    "description": "Turn on building of Kraken2 database. Requires nucleotide FASTA file input.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
+                "kraken2_keepintermediate": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-save",
+                    "description": "Retain intermediate Kraken2 build files for inspection."
                 }
             },
             "fa_icon": "fas fa-database"
diff --git a/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf b/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf
index 5916692..0c4feb8 100644
--- a/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_createtaxdb_pipeline/main.nf
@@ -193,6 +193,7 @@ def toolCitationText() {
             params.build_centrifuge ? "Centrifuge (Kim et al. 2016)," : "",
             params.build_diamond    ? "DIAMOND (Buchfink et al. 2015)," : "",
             params.build_kaiju      ? "Kaiju (Menzel et al. 2016)," : "",
+            params.build_kraken2    ? "Kraken2 (Wood et al. 2019)," : "",
             params.build_malt       ? "MALT (Vågene et al. 2018)," : "",
             "and MultiQC (Ewels et al. 2016)",
             "."
@@ -209,6 +210,7 @@ def toolBibliographyText() {
             params.build_centrifuge ? "<li>Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729.  <a href=\"https://doi.org/10.1101/gr.210641.116\">10.1101/gr.210641.116</a></li>" : "",
             params.build_diamond    ? "<li>Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59–60. <a href=\"https://doi.org/10.1038/nmeth.3176\">10.1038/nmeth.3176</a></li>" : "",
             params.build_kaiju      ? "<li>Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257. <a href=\"https://doi.org/10.1038/ncomms11257\">10.1038/ncomms11257</a></li>" : "",
+            params.build_kraken2    ? "<li>Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257.  <a href=\"https://doi.org/10.1186/s13059-019-1891-0\">10.1186/s13059-019-1891-0</a></li>" : "",
             params.build_malt       ? "<li>Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528.  <a href=\"https://doi.org/10.1038/s41559-017-0446-6\">10.1038/s41559-017-0446-6</a></li>" : "",                "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
         ].join(' ').trim()
 
diff --git a/subworkflows/nf-core/fasta_build_add_kraken2/main.nf b/subworkflows/nf-core/fasta_build_add_kraken2/main.nf
new file mode 100644
index 0000000..306896b
--- /dev/null
+++ b/subworkflows/nf-core/fasta_build_add_kraken2/main.nf
@@ -0,0 +1,35 @@
+include { KRAKEN2_ADD   } from '../../../modules/nf-core/kraken2/add/main'
+include { KRAKEN2_BUILD } from '../../../modules/nf-core/kraken2/build/main'
+
+workflow FASTA_BUILD_ADD_KRAKEN2 {
+
+    take:
+    ch_fasta              // channel: [ val(meta), fasta ]
+    ch_taxonomy_names     // channel: [ names.dmp ]
+    ch_taxonomy_nodes     // channel: [ nodes.dmp ]
+    ch_accession2taxid    // channel: [ acc2taxidfile ]
+    val_cleanintermediate // value: [ true | false ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    ch_fastas_for_kraken2add = ch_fasta
+                                .map {
+                                    meta, fasta ->
+
+                                    [[id: 'db'], fasta]
+                                }
+                                .groupTuple()
+
+    KRAKEN2_ADD ( ch_fastas_for_kraken2add, ch_taxonomy_names, ch_taxonomy_nodes, ch_accession2taxid )
+    ch_versions = ch_versions.mix(KRAKEN2_ADD.out.versions.first())
+
+    KRAKEN2_BUILD ( KRAKEN2_ADD.out.db, val_cleanintermediate )
+    ch_versions = ch_versions.mix(KRAKEN2_BUILD.out.versions.first())
+
+    emit:
+    db = KRAKEN2_BUILD.out.db // channel: [ val(meta), [ db ] ]
+    versions = ch_versions    // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/nf-core/fasta_build_add_kraken2/meta.yml b/subworkflows/nf-core/fasta_build_add_kraken2/meta.yml
new file mode 100644
index 0000000..1506709
--- /dev/null
+++ b/subworkflows/nf-core/fasta_build_add_kraken2/meta.yml
@@ -0,0 +1,61 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fasta_build_add_kraken2"
+description: KRAKEN2 build custom database subworkflow
+keywords:
+  - metagenomics
+  - kraken2
+  - database
+  - build
+  - custom
+components:
+  - kraken2/add
+  - kraken2/build
+input:
+  - ch_fasta:
+      type: file
+      description: |
+        Channel containing each fasta as a distinct element with meta
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.{fasta,fa,fna}"
+  - ch_taxonomy_names:
+      type: file
+      description: |
+        Channel containing a NCBI-style taxdump names file
+        Structure: [ names.dmp ]
+      pattern: "names.dmp"
+  - ch_taxonomy_nodes:
+      type: file
+      description: |
+        Channel containing a NCBI-style taxdump nodes file
+        Structure: [ nodes.dmp ]
+      pattern: "nodes.dmp"
+  - ch_accession2taxid:
+      type: file
+      description: |
+        Channel containing a NCBI-style taxdump accession2taxid (acc2tax) file
+        Structure: [ accession2taxid_file ]
+      pattern: "*.accession2taxid"
+  - val_cleanintermediate:
+      type: boolean
+      description: |
+        Boolean flag whether to clean up intermediate files after build or not
+        Structure: [ val_cleanintermediate ]
+      pattern: "true|false"
+output:
+  - db:
+      type: directory
+      description: |
+        Channel containing KRAKEN2 database directory.
+        Use `$ext.prefix` in a modules.conf file to change default name
+        Structure: [ val(meta), path(db) ]
+      pattern: "*/"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@jfy133"
+maintainers:
+  - "@jfy133"
diff --git a/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test b/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test
new file mode 100644
index 0000000..a7baca6
--- /dev/null
+++ b/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test
@@ -0,0 +1,103 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTA_BUILD_ADD_KRAKEN2"
+    script "../main.nf"
+    workflow "FASTA_BUILD_ADD_KRAKEN2"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fasta_build_add_kraken2"
+    tag "gunzip"
+    tag "kraken2"
+    tag "kraken2/add"
+    tag "kraken2/build"
+
+    test("metagenome - fasta") {
+
+        setup {
+            run("GUNZIP") {
+                script "modules/nf-core/gunzip/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([\
+                                [id:'haemophilus_influenzae'],
+                                file(params.modules_testdata_base_path + '/genomics/prokaryotes/metagenome/fasta/haemophilus_influenzae.fna.gz', checkIfExists: true)
+                            ]
+                    )
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([[id:'sarscov2'], file(params.modules_testdata_base_path + '/genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true)]).mix(GUNZIP.out.gunzip)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/taxdmp/names.dmp', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/taxdmp/nodes.dmp', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/accession2taxid/nucl_gb.accession2taxid', checkIfExists: true)
+                input[4] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.db.get(0).get(1) ==~ ".*/db" },
+                { assert snapshot (
+                        workflow.out.versions,
+                        path("${workflow.out.db[0][1]}/hash.k2d"),
+                        path("${workflow.out.db[0][1]}/taxo.k2d"),
+                        file("${workflow.out.db[0][1]}/opts.k2d").name,
+                        ).match()
+                }
+            )
+        }
+    }
+
+    test("metagenome - fasta - nocleanup") {
+
+        setup {
+            run("GUNZIP") {
+                script "modules/nf-core/gunzip/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([\
+                                [id:'haemophilus_influenzae'],
+                                file(params.modules_testdata_base_path + '/genomics/prokaryotes/metagenome/fasta/haemophilus_influenzae.fna.gz', checkIfExists: true)
+                            ]
+                    )
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([[id:'sarscov2'], file(params.modules_testdata_base_path + '/genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true)]).mix(GUNZIP.out.gunzip)
+                input[1] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/taxdmp/names.dmp', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/taxdmp/nodes.dmp', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/taxonomy/accession2taxid/nucl_gb.accession2taxid', checkIfExists: true)
+                input[4] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert workflow.out.db.get(0).get(1) ==~ ".*/db" },
+                { assert snapshot (
+                        workflow.out.versions,
+                        path("${workflow.out.db[0][1]}/hash.k2d"),
+                        path("${workflow.out.db[0][1]}/taxo.k2d"),
+                        file("${workflow.out.db[0][1]}/opts.k2d").name,
+                        file("${workflow.out.db[0][1]}/unmapped.txt").name
+                        ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test.snap
new file mode 100644
index 0000000..57b4a48
--- /dev/null
+++ b/subworkflows/nf-core/fasta_build_add_kraken2/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "metagenome - fasta - nocleanup": {
+        "content": [
+            [
+                "versions.yml:md5,62fb719633dd8f110bbc2c1bec53d0a9",
+                "versions.yml:md5,82f39c3ef1ba0742da3105cbe5ed3cf7"
+            ],
+            "hash.k2d:md5,4717689f8ba88d4cae51ecc7c9d9b372",
+            "taxo.k2d:md5,24338e2d78f803f48bcc5653c6e51816",
+            "opts.k2d",
+            "unmapped.txt"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-05T08:17:49.670974771"
+    },
+    "metagenome - fasta": {
+        "content": [
+            [
+                "versions.yml:md5,62fb719633dd8f110bbc2c1bec53d0a9",
+                "versions.yml:md5,82f39c3ef1ba0742da3105cbe5ed3cf7"
+            ],
+            "hash.k2d:md5,4717689f8ba88d4cae51ecc7c9d9b372",
+            "taxo.k2d:md5,24338e2d78f803f48bcc5653c6e51816",
+            "opts.k2d"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-05T08:17:31.501399396"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fasta_build_add_kraken2/tests/tags.yml b/subworkflows/nf-core/fasta_build_add_kraken2/tests/tags.yml
new file mode 100644
index 0000000..af5f2a0
--- /dev/null
+++ b/subworkflows/nf-core/fasta_build_add_kraken2/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/fasta_build_add_kraken2:
+  - subworkflows/nf-core/fasta_build_add_kraken2/**
diff --git a/tests/test.nf.test b/tests/test.nf.test
index f5c2b38..46dd23f 100644
--- a/tests/test.nf.test
+++ b/tests/test.nf.test
@@ -21,6 +21,9 @@ nextflow_pipeline {
                         path("$outputDir/centrifuge/"),
                         path("$outputDir/diamond/database.dmnd"),
                         path("$outputDir/kaiju/database.fmi"),
+                        path("$outputDir/kraken2/db/hash.k2d"),
+                        file("$outputDir/kraken2/db/opts.k2d").name,
+                        path("$outputDir/kraken2/db/taxo.k2d"),
                         path("$outputDir/malt/malt-build.log").readLines().last().contains('Peak memory'),
                         path("$outputDir/malt/malt_index/index0.idx"),
                         path("$outputDir/malt/malt_index/ref.db"),
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
index d3fe6ce..73e0d6d 100644
--- a/tests/test.nf.test.snap
+++ b/tests/test.nf.test.snap
@@ -2,26 +2,29 @@
     "test_profile": {
         "content": [
             [
-                "database.1.cf:md5,4218d7b46893c4ecfbc6919b2f072a6b",
-                "database.2.cf:md5,5b9565dc528314e931de5c03a70f3409",
-                "database.3.cf:md5,51f6eb8c75aa64cc60cd733967278866",
-                "database.4.cf:md5,954c85fd4df6ea5d37906d5027f18688"
+                "database.1.cf:md5,1481615ab90b5573f6d9e57f97890178",
+                "database.2.cf:md5,d50fa66e215e80284314ff6521dcd4a4",
+                "database.3.cf:md5,beafa92166ba461f9bda1dac0b640f45",
+                "database.4.cf:md5,2902ec5df0db6da41a91b40d2f46b30d"
             ],
             "database.dmnd:md5,b2ea49ef5490c526e2c56cae19bcb462",
             "database.fmi:md5,54fd89f5e4eab61af30175e8aa389598",
+            "hash.k2d:md5,01122a04dcef29ceb3baa68a9f6e6ef5",
+            "opts.k2d",
+            "taxo.k2d:md5,cd8170a8c5a1b763a9ac1ffa2107cc88",
             true,
             "index0.idx:md5,876139dc930e68992cd2625e08bba48a",
-            "ref.db:md5,335d4c8c7367999d79bef51882809f5f",
-            "ref.idx:md5,a07f93cdce0154d3e05e8cacc5480a3a",
+            "ref.db:md5,377073f58a9f9b85acca59fcf21744a9",
+            "ref.idx:md5,676393d0f4826dac3f47aa5290632570",
             "ref.inf:md5,446275f4f879e2b115e983db7c9ced18",
-            "taxonomy.idx:md5,309f2a558c08f551fc939e749fd42fd8",
+            "taxonomy.idx:md5,1e2e8fdc703a6d2707e7cbefd2b6d93f",
             "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0",
             "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e"
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.02.0"
         },
-        "timestamp": "2024-02-15T11:47:20.945591503"
+        "timestamp": "2024-04-11T10:59:28.687364796"
     }
 }
\ No newline at end of file
diff --git a/workflows/createtaxdb.nf b/workflows/createtaxdb.nf
index f635d34..ea8c59a 100644
--- a/workflows/createtaxdb.nf
+++ b/workflows/createtaxdb.nf
@@ -11,6 +11,7 @@ include { CENTRIFUGE_BUILD                   } from '../modules/nf-core/centrifu
 include { KAIJU_MKFMI                        } from '../modules/nf-core/kaiju/mkfmi/main'
 include { DIAMOND_MAKEDB                     } from '../modules/nf-core/diamond/makedb/main'
 include { MALT_BUILD                         } from '../modules/nf-core/malt/build/main'
+include { GUNZIP as GUNZIP_DNA               } from '../modules/nf-core/gunzip/main'
 include { PIGZ_COMPRESS as PIGZ_COMPRESS_DNA } from '../modules/nf-core/pigz/compress/main'
 include { PIGZ_COMPRESS as PIGZ_COMPRESS_AA  } from '../modules/nf-core/pigz/compress/main'
 include { UNZIP                              } from '../modules/nf-core/unzip/main'
@@ -20,6 +21,7 @@ include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pi
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_createtaxdb_pipeline'
 
+include { FASTA_BUILD_ADD_KRAKEN2 } from '../subworkflows/nf-core/fasta_build_add_kraken2/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -30,16 +32,28 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_crea
 workflow CREATETAXDB {
 
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet       // channel: samplesheet read in from --input
+    ch_taxonomy_namesdmp // channel: taxonomy names file
+    ch_taxonomy_nodesdmp // channel: taxonomy nodes file
+    ch_accession2taxid   // channel: accession2taxid file
+    ch_nucl2taxid        // channel: nucl2taxid file
+    ch_prot2taxid        // channel: prot2taxid file
+    ch_malt_mapdb        // channel: maltmap file
 
     main:
 
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    DATA PREPARATION
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
     // PREPARE: Prepare input for single file inputs modules
 
-    if ( [params.build_malt, params.build_centrifuge].any() ) {  // Pull just DNA sequences
+    if ( [params.build_malt, params.build_centrifuge, params.build_kraken2].any() ) {  // Pull just DNA sequences
 
         ch_dna_refs_for_singleref = ch_samplesheet
                                         .map{meta, fasta_dna, fasta_aa  -> [[id: params.dbname], fasta_dna]}
@@ -47,16 +61,16 @@ workflow CREATETAXDB {
                                             fasta_dna
                                         }
 
-        ch_dna_for_zipping = ch_dna_refs_for_singleref
+        ch_dna_for_unzipping = ch_dna_refs_for_singleref
                                 .branch {
                                     meta, fasta ->
                                         zipped: fasta.extension == 'gz'
                                         unzipped: true
                                 }
 
-        PIGZ_COMPRESS_DNA ( ch_dna_for_zipping.unzipped )
-
-        ch_prepped_dna_fastas = PIGZ_COMPRESS_DNA.out.archive.mix(ch_dna_for_zipping.zipped).groupTuple()
+        GUNZIP_DNA ( ch_dna_for_unzipping.zipped )
+        ch_prepped_dna_fastas = GUNZIP_DNA.out.gunzip.mix(ch_dna_for_unzipping.unzipped).groupTuple()
+        ch_versions = ch_versions.mix(GUNZIP_DNA.out.versions.first())
 
         // Place in single file
         ch_singleref_for_dna = CAT_CAT_DNA ( ch_prepped_dna_fastas )
@@ -84,28 +98,40 @@ workflow CREATETAXDB {
                                 }
 
         PIGZ_COMPRESS_AA ( ch_aa_for_zipping.unzipped )
-
         ch_prepped_aa_fastas = PIGZ_COMPRESS_AA.out.archive.mix(ch_aa_for_zipping.zipped).groupTuple()
+        //ch_versions = ch_versions.mix( PIGZ_COMPRESS_AA.versions.first() )
 
         ch_singleref_for_aa = CAT_CAT_AA ( ch_prepped_aa_fastas )
-        ch_versions = ch_versions.mix(CAT_CAT_AA.out.versions.first())
+        ch_versions = ch_versions.mix( CAT_CAT_AA.out.versions.first() )
+    }
+
+    /*
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    DATABASE BUILDING
+    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    */
+
+    // Module: Run CENTRIFUGE/BUILD
+
+    if ( params.build_centrifuge ) {
+        CENTRIFUGE_BUILD ( CAT_CAT_DNA.out.file_out, ch_nucl2taxid, ch_taxonomy_nodesdmp, ch_taxonomy_namesdmp, [] )
+        ch_versions = ch_versions.mix(CENTRIFUGE_BUILD.out.versions.first())
+        ch_centrifuge_output = CENTRIFUGE_BUILD.out.cf
+    } else {
+        ch_centrifuge_output = Channel.empty()
     }
 
-    //
     // MODULE: Run DIAMOND/MAKEDB
-    //
 
     if ( params.build_diamond  ) {
-        DIAMOND_MAKEDB ( CAT_CAT_AA.out.file_out, params.prot2taxid, params.nodesdmp, params.namesdmp )
+        DIAMOND_MAKEDB ( CAT_CAT_AA.out.file_out, ch_prot2taxid, ch_taxonomy_nodesdmp, ch_taxonomy_namesdmp )
         ch_versions = ch_versions.mix(DIAMOND_MAKEDB.out.versions.first())
         ch_diamond_output = DIAMOND_MAKEDB.out.db
     } else {
         ch_diamond_output = Channel.empty()
     }
 
-    //
     // MODULE: Run KAIJU/MKFMI
-    //
 
     if ( params.build_kaiju ) {
         KAIJU_MKFMI ( CAT_CAT_AA.out.file_out )
@@ -115,19 +141,16 @@ workflow CREATETAXDB {
         ch_kaiju_output = Channel.empty()
     }
 
-    // Module: Run CENTRIFUGE/BUILD
-
-    if ( params.build_centrifuge ) {
-        CENTRIFUGE_BUILD ( CAT_CAT_DNA.out.file_out, params.nucl2taxid, params.nodesdmp, params.namesdmp, [] )
-        ch_versions = ch_versions.mix(CENTRIFUGE_BUILD.out.versions.first())
-        ch_centrifuge_output = CENTRIFUGE_BUILD.out.cf
+    // SUBWORKFLOW: Kraken2
+    if ( params.build_kraken2 ) {
+        FASTA_BUILD_ADD_KRAKEN2 ( CAT_CAT_DNA.out.file_out, ch_taxonomy_namesdmp, ch_taxonomy_nodesdmp, ch_accession2taxid, !params.kraken2_keepintermediate )
+        ch_versions = ch_versions.mix(FASTA_BUILD_ADD_KRAKEN2.out.versions.first())
+        ch_kraken2_output = FASTA_BUILD_ADD_KRAKEN2.out.db
     } else {
-        ch_centrifuge_output = Channel.empty()
+        ch_kraken2_output = Channel.empty()
     }
 
-    //
     // Module: Run MALT/BUILD
-    //
 
     if ( params.build_malt ) {
 
@@ -186,6 +209,7 @@ workflow CREATETAXDB {
     centrifuge_database = ch_centrifuge_output
     diamond_database    = ch_diamond_output
     kaiju_database      = ch_kaiju_output
+    kraken2_database    = ch_kraken2_output
     malt_database       = ch_malt_output
 }