diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7e6eb7b4..480c2c5d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,17 +23,19 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #405](https://github.com/nf-core/viralrecon/pull/412)] - Including parameter `depthcutoff` to freyja demix and boot
 - [[PR #413](https://github.com/nf-core/viralrecon/pull/413)] - Update multiqc module & include freyja in report
 - [[PR #401](https://github.com/nf-core/viralrecon/pull/401)] - Added option to add a custom annotation
+- [[PR #417](https://github.com/nf-core/viralrecon/pull/417)] - Allow skipping of Freyja bootstrapping module & freyja module update
 
 ### Parameters
 
-| Old parameter       | New parameter             |
-| ------------------- | ------------------------- |
-| `--skip_freyja`     |                           |
-| `--freyja_repeats`  |                           |
-| `--freyja_db_name`  |                           |
-| `--freyja_barcodes` |                           |
-| `--freyja_lineages` |                           |
-|                     | `--additional_annotation` |
+| Old parameter | New parameter             |
+| ------------- | ------------------------- |
+|               | `--skip_freyja`           |
+|               | `--freyja_repeats`        |
+|               | `--freyja_db_name`        |
+|               | `--freyja_barcodes`       |
+|               | `--freyja_lineages`       |
+|               | `--skip_freyja_boot`      |
+|               | `--additional_annotation` |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
@@ -45,7 +47,7 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
-| `freyja`   |             | 1.3.12      |
+| `freyja`   |             | 1.5.0       |
 | `multiqc`  | 1.14        | 1.19        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.
diff --git a/docs/usage.md b/docs/usage.md
index c5aacc24..ac7f5e5b 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -317,7 +317,7 @@ To learn how to provide additional arguments to a particular tool of the pipelin
 
 #### Freyja
 
-[Freyja](https://github.com/andersen-lab/Freyja) relies on a dataset of barcodes that use lineage defining mutations (see [UShER](https://usher-wiki.readthedocs.io/en/latest/#)). By default the most recent barcodes will be downloaded and used. However, if analyses need to be compared across multiple datasets, it might be of interest to re-use the same barcodes, or to rerun all Freyja analyses with the most recent dataset. To do this, specify the barcodes and lineages using the `--freyja_barcodes`, `--freyja_lineages` parameters, respectivly.
+[Freyja](https://github.com/andersen-lab/Freyja) relies on a dataset of barcodes that use lineage defining mutations (see [UShER](https://usher-wiki.readthedocs.io/en/latest/#)). By default the most recent barcodes will be downloaded and used. However, if analyses need to be compared across multiple datasets, it might be of interest to re-use the same barcodes, or to rerun all Freyja analyses with the most recent dataset. To do this, specify the barcodes and lineages using the `--freyja_barcodes`, `--freyja_lineages` parameters, respectivly. The boostrapping of Freyja can be skipped by specifying `--skip_freyja_boot`.
 
 ### nf-core/configs
 
diff --git a/modules.json b/modules.json
index 52526931..b529c5b6 100644
--- a/modules.json
+++ b/modules.json
@@ -117,22 +117,22 @@
                     },
                     "freyja/boot": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/demix": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/update": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "freyja/variants": {
                         "branch": "master",
-                        "git_sha": "7e33bdd8b4faf45be1be6a6f49979f0f0820d243",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["bam_variant_demix_boot_freyja"]
                     },
                     "gunzip": {
@@ -296,7 +296,7 @@
                     },
                     "bam_variant_demix_boot_freyja": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "5a30449ceb86c4f968fc5425a020b9e5809c9c5c",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_align_bowtie2": {
@@ -311,7 +311,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/freyja/boot/environment.yml b/modules/nf-core/freyja/boot/environment.yml
index 71c285aa..dfab14ec 100644
--- a/modules/nf-core/freyja/boot/environment.yml
+++ b/modules/nf-core/freyja/boot/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::freyja=1.4.7
+  - bioconda::freyja=1.5.0
diff --git a/modules/nf-core/freyja/boot/main.nf b/modules/nf-core/freyja/boot/main.nf
index 7d35c06a..ca1f1a35 100644
--- a/modules/nf-core/freyja/boot/main.nf
+++ b/modules/nf-core/freyja/boot/main.nf
@@ -5,8 +5,8 @@ process FREYJA_BOOT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.4.7--pyhdfd78af_0':
-        'biocontainers/freyja:1.4.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
+        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(variants), path(depths)
diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test b/modules/nf-core/freyja/boot/tests/main.nf.test
index 6f75a9c6..f9efb2df 100644
--- a/modules/nf-core/freyja/boot/tests/main.nf.test
+++ b/modules/nf-core/freyja/boot/tests/main.nf.test
@@ -9,7 +9,7 @@ nextflow_process {
     tag "freyja"
     tag "freyja/boot"
     tag "freyja/variants"
-    tag "freyja/updatedb"
+    tag "freyja/update"
 
     test("sarscov2 - illumina - test_paired_end_sorted - bam") {
 
@@ -40,7 +40,7 @@ nextflow_process {
             process {
                 """
                 input[0] = FREYJA_VARIANTS.out.variants
-                input[1] = 10
+                input[1] = 3
                 input[2] = FREYJA_UPDATE.out.barcodes
                 input[3] = FREYJA_UPDATE.out.lineages_meta
                 """
diff --git a/modules/nf-core/freyja/boot/tests/main.nf.test.snap b/modules/nf-core/freyja/boot/tests/main.nf.test.snap
index b6143310..334c743f 100644
--- a/modules/nf-core/freyja/boot/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/boot/tests/main.nf.test.snap
@@ -2,9 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,0cf7253a5b3b16532fca5908dffb01b8"
+                "versions.yml:md5,a2af061943f186aa529b80a419a8fcc1"
             ]
         ],
-        "timestamp": "2023-12-06T15:36:42.746574889"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:10:15.064948172"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/freyja/demix/environment.yml b/modules/nf-core/freyja/demix/environment.yml
index d692468f..0f29b8ce 100644
--- a/modules/nf-core/freyja/demix/environment.yml
+++ b/modules/nf-core/freyja/demix/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::freyja=1.4.7
+  - bioconda::freyja=1.5.0
diff --git a/modules/nf-core/freyja/demix/main.nf b/modules/nf-core/freyja/demix/main.nf
index 9ea5bdd4..0ae3246b 100644
--- a/modules/nf-core/freyja/demix/main.nf
+++ b/modules/nf-core/freyja/demix/main.nf
@@ -5,8 +5,8 @@ process FREYJA_DEMIX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.4.7--pyhdfd78af_0':
-        'biocontainers/freyja:1.4.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
+        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(variants), path(depths)
diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test b/modules/nf-core/freyja/demix/tests/main.nf.test
index 6ad1fb4a..df25d82b 100644
--- a/modules/nf-core/freyja/demix/tests/main.nf.test
+++ b/modules/nf-core/freyja/demix/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "freyja"
     tag "freyja/demix"
     tag "freyja/variants"
-    tag "freyja/updatedb"
+    tag "freyja/update"
 
     test("sarscov2 - illumina - test_paired_end_sorted - bam") {
 
diff --git a/modules/nf-core/freyja/demix/tests/main.nf.test.snap b/modules/nf-core/freyja/demix/tests/main.nf.test.snap
index e4d3fad5..f36e9cc6 100644
--- a/modules/nf-core/freyja/demix/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/demix/tests/main.nf.test.snap
@@ -2,9 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,d36ecae032c1b476d7b57de248b72729"
+                "versions.yml:md5,a9c5d4ae8f93de8cbc08c7d87debd89c"
             ]
         ],
-        "timestamp": "2023-12-06T13:37:14.56803127"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:10:46.778891705"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/freyja/update/environment.yml b/modules/nf-core/freyja/update/environment.yml
index 7d7b1e9b..9dbffbb6 100644
--- a/modules/nf-core/freyja/update/environment.yml
+++ b/modules/nf-core/freyja/update/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::freyja=1.4.7
+  - bioconda::freyja=1.5.0
diff --git a/modules/nf-core/freyja/update/main.nf b/modules/nf-core/freyja/update/main.nf
index eb320b35..4d4b6857 100644
--- a/modules/nf-core/freyja/update/main.nf
+++ b/modules/nf-core/freyja/update/main.nf
@@ -5,8 +5,8 @@ process FREYJA_UPDATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.4.7--pyhdfd78af_0':
-        'biocontainers/freyja:1.4.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
+        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
 
     input:
     val db_name
diff --git a/modules/nf-core/freyja/update/tests/main.nf.test.snap b/modules/nf-core/freyja/update/tests/main.nf.test.snap
index 6eae23e0..0f510c62 100644
--- a/modules/nf-core/freyja/update/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/update/tests/main.nf.test.snap
@@ -2,9 +2,13 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,8649650231828547e8fed40e072da108"
+                "versions.yml:md5,c730cb8a7d262beaace190a3e832a54d"
             ]
         ],
-        "timestamp": "2023-12-06T14:13:14.806958334"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:11:08.501478371"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/freyja/variants/environment.yml b/modules/nf-core/freyja/variants/environment.yml
index 4fb28982..871a0745 100644
--- a/modules/nf-core/freyja/variants/environment.yml
+++ b/modules/nf-core/freyja/variants/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::freyja=1.4.7
+  - bioconda::freyja=1.5.0
diff --git a/modules/nf-core/freyja/variants/main.nf b/modules/nf-core/freyja/variants/main.nf
index e319114b..fc876971 100644
--- a/modules/nf-core/freyja/variants/main.nf
+++ b/modules/nf-core/freyja/variants/main.nf
@@ -5,8 +5,8 @@ process FREYJA_VARIANTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/freyja:1.4.7--pyhdfd78af_0':
-        'biocontainers/freyja:1.4.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/freyja:1.5.0--pyhdfd78af_0':
+        'biocontainers/freyja:1.5.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/freyja/variants/tests/main.nf.test.snap b/modules/nf-core/freyja/variants/tests/main.nf.test.snap
index 2693e2f9..c85e8032 100644
--- a/modules/nf-core/freyja/variants/tests/main.nf.test.snap
+++ b/modules/nf-core/freyja/variants/tests/main.nf.test.snap
@@ -13,7 +13,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,f7edb34ea4dfc2fbb2299aef03791926"
+                    "versions.yml:md5,10000e2412ba93678d3a4345fd98a2e3"
                 ],
                 "variants": [
                     [
@@ -26,10 +26,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f7edb34ea4dfc2fbb2299aef03791926"
+                    "versions.yml:md5,10000e2412ba93678d3a4345fd98a2e3"
                 ]
             }
         ],
-        "timestamp": "2023-12-06T15:13:57.445426554"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:11:32.315489497"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 0645edac..5a5b50e1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -43,6 +43,7 @@ params {
     multiqc_config             = null
     max_multiqc_email_size     = '25.MB'
     skip_freyja                = false
+    skip_freyja_boot           = false
     freyja_repeats             = 100
     freyja_depthcutoff         = null
     freyja_db_name             = 'freyja_db'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7e6ccbd3..e69110b3 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -265,6 +265,11 @@
                     "fa_icon": "fas fa-forward",
                     "description": "Skip freyja deep SARS-CoV-2 variant analysis using a depth weighted approach."
                 },
+                "skip_freyja_boot": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-forward",
+                    "description": "Skip the bootstrapping  module of Freyja"
+                },
                 "freyja_db_name": {
                     "type": "string",
                     "default": "freyja_db",
@@ -281,7 +286,8 @@
                     "type": "integer",
                     "default": 100,
                     "fa_icon": "fas fa-hand-paper",
-                    "description": "Specify the number of bootstrap repeats to do."
+                    "description": "Specify the number of bootstrap repeats to do.",
+                    "minimum": 1
                 },
                 "freyja_barcodes": {
                     "type": "string",
diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf b/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf
index 12c967ed..ad1fdc08 100644
--- a/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf
+++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/main.nf
@@ -8,6 +8,7 @@ workflow BAM_VARIANT_DEMIX_BOOT_FREYJA {
     take:
     ch_bam              // channel: [ val(meta), path(bam) ]
     ch_fasta            // channel: [ path(fasta) ]
+    val_skip_boot       // value skip_boot
     val_repeats         // value repeats
     val_db_name         // string db_name
     ch_barcodes         // channel:  [ path(barcodes)]
@@ -24,8 +25,7 @@ workflow BAM_VARIANT_DEMIX_BOOT_FREYJA {
         ch_fasta
     )
     ch_freyja_variants = FREYJA_VARIANTS.out.variants
-
-    ch_versions = ch_versions.mix(FREYJA_VARIANTS.out.versions.first())
+    ch_versions        = ch_versions.mix(FREYJA_VARIANTS.out.versions.first())
 
     //
     // Update the database if none are given.
@@ -34,11 +34,9 @@ workflow BAM_VARIANT_DEMIX_BOOT_FREYJA {
         FREYJA_UPDATE (
             val_db_name
         )
-
         ch_barcodes      = FREYJA_UPDATE.out.barcodes
         ch_lineages_meta = FREYJA_UPDATE.out.lineages_meta
-
-        ch_versions = ch_versions.mix(FREYJA_UPDATE.out.versions.first())
+        ch_versions      = ch_versions.mix(FREYJA_UPDATE.out.versions.first())
     }
 
 
@@ -51,25 +49,31 @@ workflow BAM_VARIANT_DEMIX_BOOT_FREYJA {
         ch_lineages_meta
     )
     ch_freyja_demix = FREYJA_DEMIX.out.demix
-    ch_versions = ch_versions.mix(FREYJA_DEMIX.out.versions.first())
+    ch_versions     = ch_versions.mix(FREYJA_DEMIX.out.versions.first())
 
 
     //
     // Perform bootstrapping to get more accurate estimates of abundancies
     //
-    FREYJA_BOOT (
-        ch_freyja_variants,
-        val_repeats,
-        ch_barcodes,
-        ch_lineages_meta
-    )
-    ch_versions = ch_versions.mix(FREYJA_BOOT.out.versions.first())
+    ch_lineages   = Channel.empty()
+    ch_summarized = Channel.empty()
+    if (!val_skip_boot){
+        FREYJA_BOOT (
+            ch_freyja_variants,
+            val_repeats,
+            ch_barcodes,
+            ch_lineages_meta
+        )
+        ch_lineages   = FREYJA_BOOT.out.lineages
+        ch_summarized = FREYJA_BOOT.out.summarized
+        ch_versions   = ch_versions.mix(FREYJA_BOOT.out.versions.first())
+    }
 
     emit:
     variants       = FREYJA_VARIANTS.out.variants  // channel: [ val(meta), path(variants_tsv), path(depths_tsv) ]
     demix          = FREYJA_DEMIX.out.demix        // channel: [ val(meta), path(demix_tsv) ]
-    lineages       = FREYJA_BOOT.out.lineages      // channel: [ val(meta), path(lineages_csv) ]
-    summarized     = FREYJA_BOOT.out.summarized    // channel: [ val(meta), path(summarized_csv) ]
+    lineages       = ch_lineages                   // channel: [ val(meta), path(lineages_csv) ]
+    summarized     = ch_summarized                 // channel: [ val(meta), path(summarized_csv) ]
     barcodes       = ch_barcodes                   // channel: [ path(barcodes) ]
     lineages_meta  = ch_lineages_meta              // channel: [ path(lineages_meta) ]
     versions       = ch_versions                   // channel: [ path(versions.yml) ]
diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test
new file mode 100644
index 00000000..8ea5c8ba
--- /dev/null
+++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test
@@ -0,0 +1,127 @@
+nextflow_workflow {
+
+    name "Test Workflow BAM_VARIANT_DEMIX_BOOT_FREYJA"
+    script "../main.nf"
+    workflow "BAM_VARIANT_DEMIX_BOOT_FREYJA"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "bam_variant_demix_boot_freyja"
+    tag "subworkflows/bam_variant_demix_boot_freyja"
+    tag "freyja"
+    tag "freyja/variants"
+    tag "freyja/update"
+    tag "freyja/demix"
+    tag "freyja/boot"
+
+    test("sarscov2 - bam - val - nodb"){
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                      file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
+                input[2] = false
+                input[3] = 3
+                input[4] = 'freyja_db'
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out.variants,
+                                  workflow.out.versions).match() },
+                // All depend on a database that gets updated regularly
+                { assert path(workflow.out.demix.get(0).get(1)).getText().contains("summarized") },
+                { assert path(workflow.out.summarized.get(0).get(1)).getText().contains("0.025,") },
+                { assert path(workflow.out.lineages.get(0).get(1)).getText().contains("0.025,") },
+                { assert path(workflow.out.barcodes.get(0)).exists() },
+                { assert path(workflow.out.lineages_meta.get(0)).exists() },
+            )
+        }
+    }
+
+    test("sarscov2 - bam - val - db"){
+
+        setup {
+            run("FREYJA_UPDATE") {
+                script "../../../../modules/nf-core/freyja/update/main.nf"
+                process {
+                    """
+                    input[0] = "test_db"
+                    """
+                }
+            }
+        }
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                      file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
+                input[2] = false
+                input[3] = 3
+                input[4] = 'test_db'
+                input[5] = FREYJA_UPDATE.out.barcodes
+                input[6] = FREYJA_UPDATE.out.lineages_meta
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out.variants,
+                                  workflow.out.versions).match() },
+                // All depend on a database that gets updated regularly
+                { assert path(workflow.out.demix.get(0).get(1)).getText().contains("summarized") },
+                { assert path(workflow.out.summarized.get(0).get(1)).getText().contains("0.025,") },
+                { assert path(workflow.out.lineages.get(0).get(1)).getText().contains("0.025,") },
+                { assert path(workflow.out.barcodes.get(0)).exists() },
+                { assert path(workflow.out.lineages_meta.get(0)).exists() },
+            )
+        }
+    }
+
+    test("sarscov2 - bam - skip - val - nodb"){
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                      file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                ])
+                input[1] = Channel.of([file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)])
+                input[2] = true
+                input[3] = 0
+                input[4] = 'test_db'
+                input[5] = []
+                input[6] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(workflow.out.variants,
+                                  workflow.out.versions).match() },
+                // All depend on a database that gets updated regularly
+                { assert path(workflow.out.demix.get(0).get(1)).getText().contains("summarized") },
+                { assert path(workflow.out.barcodes.get(0)).exists() },
+                { assert path(workflow.out.lineages_meta.get(0)).exists() },
+            )
+        }
+    }
+
+}
diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap
new file mode 100644
index 00000000..c16d8793
--- /dev/null
+++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/main.nf.test.snap
@@ -0,0 +1,75 @@
+{
+    "sarscov2 - bam - val - db": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.variants.tsv:md5,966450bae4d9abae278572927b821983",
+                    "test.depth.tsv:md5,27f79b28a365a8af915895b484d1153e"
+                ]
+            ],
+            [
+                "versions.yml:md5,d3e911c025e35de092f7ef0073ccf807",
+                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
+                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:12:55.505491641"
+    },
+    "sarscov2 - bam - skip - val - nodb": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.variants.tsv:md5,966450bae4d9abae278572927b821983",
+                    "test.depth.tsv:md5,27f79b28a365a8af915895b484d1153e"
+                ]
+            ],
+            [
+                "versions.yml:md5,4b7dccb03c75e8e94d7c6bdefaa90c95",
+                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
+                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:13:29.413908034"
+    },
+    "sarscov2 - bam - val - nodb": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.variants.tsv:md5,966450bae4d9abae278572927b821983",
+                    "test.depth.tsv:md5,27f79b28a365a8af915895b484d1153e"
+                ]
+            ],
+            [
+                "versions.yml:md5,4b7dccb03c75e8e94d7c6bdefaa90c95",
+                "versions.yml:md5,d3e911c025e35de092f7ef0073ccf807",
+                "versions.yml:md5,df54ea89f3bcb7e5952e7e3dae1d22a4",
+                "versions.yml:md5,e66aeb30f8646d583bec6fbf4fe02426"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T16:12:09.796799525"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/tags.yml b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/tags.yml
new file mode 100644
index 00000000..f0c88761
--- /dev/null
+++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/bam_variant_demix_boot_freyja:
+  - subworkflows/nf-core/bam_variant_demix_boot_freyja/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
diff --git a/workflows/illumina.nf b/workflows/illumina.nf
index d2cf6171..7de8bbe4 100644
--- a/workflows/illumina.nf
+++ b/workflows/illumina.nf
@@ -472,6 +472,7 @@ workflow ILLUMINA {
         BAM_VARIANT_DEMIX_BOOT_FREYJA(
             ch_bam,
             PREPARE_GENOME.out.fasta,
+            params.skip_freyja_boot,
             params.freyja_repeats,
             params.freyja_db_name,
             params.freyja_barcodes,
diff --git a/workflows/nanopore.nf b/workflows/nanopore.nf
index 08bb9e0b..a46fca24 100644
--- a/workflows/nanopore.nf
+++ b/workflows/nanopore.nf
@@ -459,6 +459,7 @@ workflow NANOPORE {
         BAM_VARIANT_DEMIX_BOOT_FREYJA(
             ARTIC_MINION.out.bam_primertrimmed,
             PREPARE_GENOME.out.fasta,
+            params.skip_freyja_boot,
             params.freyja_repeats,
             params.freyja_db_name,
             params.freyja_barcodes,