diff --git a/CHANGELOG.md b/CHANGELOG.md
index f2d79a65..fd59f4b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,14 @@ description: A full list of Bactopia releases and a description of the changes.
 - phispy not working with Bakta genbank files
 - missed check of `--download_bakta` param in main workflow
 - quast not working when estimated genome size is 0
+- `abricate` now gets database subdirectories
+
+### `Enhancements to OSS`
+
+- fix amrfinderplus pinning in abritamr [bioconda/bioconda-recipes#46714](https://github.com/bioconda/bioconda-recipes/pull/46714)
+- adjust python pinning in gubbins [bioconda/bioconda-recipes#46713](https://github.com/bioconda/bioconda-recipes/pull/46713)
+- fix issue with sistr container [bioconda/bioconda-recipes#46712](https://github.com/bioconda/bioconda-recipes/pull/46712)
+- update rgi pinning for pyrodigal [bioconda/bioconda-recipes#46669](https://github.com/bioconda/bioconda-recipes/pull/46669)
 
 ## v3.0.0 bactopia/bactopia "Black Cat and Brown Dog" - 2023/09/11
 
diff --git a/bin/scrubber-summary.py b/bin/scrubber-summary.py
new file mode 100755
index 00000000..01337a17
--- /dev/null
+++ b/bin/scrubber-summary.py
@@ -0,0 +1,59 @@
+#! /usr/bin/env python3
+"""
+Create a simple before and after report from scrubbing
+"""
+PROGRAM = "scrubber-summary"
+VERSION = "3.0.1"
+import json
+import sys
+
+def read_json(json_file):
+    json_data = None
+    with open(json_file, 'rt') as json_fh:
+        json_data = json.load(json_fh)
+    return json_data
+
+if __name__ == '__main__':
+    import argparse as ap
+
+    parser = ap.ArgumentParser(
+        prog=PROGRAM,
+        conflict_handler='resolve',
+        description=(
+            f'{PROGRAM} (v{VERSION}) - Create a simple before and after report from scrubbing'
+        )
+    )
+    parser.add_argument('sample', metavar="SAMPLE", type=str,
+                        help='the name of the sample')
+    parser.add_argument('original', metavar="ORIGINAL", type=str,
+                        help='A summary of the original FASTQs in JSON format')
+    parser.add_argument('scrubbed', metavar="SCRUBBED", type=str,
+                        help='A summary of the scrubbed FASTQs in JSON format')
+    parser.add_argument('--version', action='version',
+                        version=f'{PROGRAM} {VERSION}')
+
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(0)
+
+    args = parser.parse_args()
+
+    original_json = read_json(args.original)
+    scrubbed_json = read_json(args.scrubbed)
+
+    # Summary
+    cols = [
+        'sample',
+        'original_read_total',
+        'scrubbed_read_total',
+        'host_read_total',
+    ]
+    results = [
+        args.sample,
+        str(original_json['qc_stats']['read_total']),
+        str(scrubbed_json['qc_stats']['read_total']),
+        str(original_json['qc_stats']['read_total'] - scrubbed_json['qc_stats']['read_total']),
+    ]
+
+    print('\t'.join(cols))
+    print('\t'.join(results))
diff --git a/conf/params.config b/conf/params.config
index 576f0abb..8b3fd69c 100644
--- a/conf/params.config
+++ b/conf/params.config
@@ -13,7 +13,7 @@ params {
 
     //nf-core
     schema_ignore_params = 'no_check_certificate,run_name,prokka_debug,is_ci,sourmash_url,mash_url,mlst_url,amrfinder_url,merge_folder,wf_has_subdir,build_all,use_mamba,empty_proteins,empty_tf,empty_adapters,empty_phix,help_all,include_tools,min_time,publish_dir,silent,test_data,test_data_dir,verbose,schema_inputs,empty_extra,empty_r2,empty_r1,workflows,available_workflows,is_subworkflow,enable_conda,force_rebuild,config_profile_url,config_profile_contact,config_profile_description,config_profile_name'
-    schema_inputs = ['fastqs', 'R1,R2,SE,sample,hybrid', 'R1,R2,sample', 'SE,sample', 'assembly,sample', 'accessions', 'accession']
+    schema_inputs = ['fastqs', 'r1,r2,se,sample,hybrid', 'r1,r2,sample', 'se,sample', 'assembly,sample', 'accessions', 'accession']
 
     // Max Job Request Parameters
     max_retry = 3
diff --git a/modules/nf-core/abritamr/run/main.nf b/modules/nf-core/abritamr/run/main.nf
index eba448c0..1e16fe10 100644
--- a/modules/nf-core/abritamr/run/main.nf
+++ b/modules/nf-core/abritamr/run/main.nf
@@ -13,8 +13,8 @@ process ABRITAMR_RUN {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/abritamr:1.0.17--pyh5707d69_0' :
-        'quay.io/biocontainers/abritamr:1.0.17--pyh5707d69_0' }"
+        'https://depot.galaxyproject.org/singularity/abritamr:1.0.17--pyh5707d69_1' :
+        'quay.io/biocontainers/abritamr:1.0.17--pyh5707d69_1' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/ariba/getref/main.nf b/modules/nf-core/ariba/getref/main.nf
index 3a8f31e9..9be54cb2 100644
--- a/modules/nf-core/ariba/getref/main.nf
+++ b/modules/nf-core/ariba/getref/main.nf
@@ -14,8 +14,8 @@ process ARIBA_GETREF {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_3' :
-        'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_3' }"
+        'https://depot.galaxyproject.org/singularity/ariba:2.14.6--py39h67e14b5_4' :
+        'quay.io/biocontainers/ariba:2.14.6--py39h67e14b5_4' }"
 
     input:
     val(db_name)
diff --git a/modules/nf-core/busco/params.config b/modules/nf-core/busco/params.config
index b29a3950..16efe4bb 100644
--- a/modules/nf-core/busco/params.config
+++ b/modules/nf-core/busco/params.config
@@ -13,5 +13,5 @@ params {
     augustus_parameters = ""
     augustus_species = ""
     augustus_long = false
-    run_name = params.busco_lineage
+    run_name = "${params.wf}-${params.busco_lineage}"
 }
diff --git a/modules/nf-core/custom/wget/main.nf b/modules/nf-core/custom/wget/main.nf
new file mode 100644
index 00000000..65e0b600
--- /dev/null
+++ b/modules/nf-core/custom/wget/main.nf
@@ -0,0 +1,35 @@
+// Import generic module functions
+include { get_resources; initOptions; saveFiles } from '../../../../lib/nf/functions'
+RESOURCES     = get_resources(workflow.profile, params.max_memory, params.max_cpus)
+options       = initOptions(params.containsKey("options") ? params.options : [:], 'custom_wget')
+options.btype = options.btype ?: "comparative"
+conda_tools   = "bioconda::gnu-wget=1.18"
+conda_name    = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
+conda_env     = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
+
+process CUSTOM_WGET {
+    label 'process_low'
+    storeDir params.datasets_cache
+    publishDir params.datasets_cache
+
+    conda (params.enable_conda ? conda_env : null)
+    container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gnu-wget:1.18--h36e9172_9' :
+        'quay.io/biocontainers/gnu-wget:1.18--h36e9172_9' }"
+
+    output:
+    path "${options.args2}", emit: download
+    path "*.{log,err}"   , emit: logs, optional: true
+    path ".command.*"    , emit: nf_logs
+    path "versions.yml"  ,emit: versions
+
+    script:
+    """
+    wget $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wget: \$(echo \$( wget --version 2>&1) | sed "s/GNU Wget //;s/ .*//;" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/custom/wget/meta.yaml b/modules/nf-core/custom/wget/meta.yaml
new file mode 100644
index 00000000..fdfa03ba
--- /dev/null
+++ b/modules/nf-core/custom/wget/meta.yaml
@@ -0,0 +1,24 @@
+name: custom_wget
+description: Custom module used to download files using wget
+keywords:
+  - wget
+  - custom
+  - version
+tools:
+  - custom:
+      description: Custom module used to download files using wget
+      homepage: https://github.com/nf-core/tools
+      documentation: https://github.com/nf-core/tools
+
+output:
+  - download:
+      type: file
+      description: Downloaded file from input URL
+      pattern: "*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@rpetit3"
diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf
index 20797b2f..3ef725cc 100644
--- a/modules/nf-core/gubbins/main.nf
+++ b/modules/nf-core/gubbins/main.nf
@@ -13,8 +13,8 @@ process GUBBINS {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gubbins:3.3.4--py310pl5321he4a0461_0' :
-        'quay.io/biocontainers/gubbins:3.3.4--py310pl5321he4a0461_0' }"
+        'https://depot.galaxyproject.org/singularity/gubbins:3.3.4--py39pl5321he4a0461_1' :
+        'quay.io/biocontainers/gubbins:3.3.4--py39pl5321he4a0461_1' }"
 
     input:
     tuple val(meta), path(msa)
diff --git a/modules/nf-core/kraken2/main.nf b/modules/nf-core/kraken2/main.nf
index 768dc723..ef8923b3 100644
--- a/modules/nf-core/kraken2/main.nf
+++ b/modules/nf-core/kraken2/main.nf
@@ -32,9 +32,9 @@ process KRAKEN2 {
     script:
     prefix = options.suffix ? "${options.suffix}" : "${meta.id}"
     def paired = meta.single_end ? "" : "--paired"
-    classified_naming = params.wf == "teton" ? "host" : "classified"
+    classified_naming = params.wf == "teton" || params.wf == "scrubber" ? "host" : "classified"
     classified = meta.single_end ? "${prefix}.${classified_naming}.fastq"   : "${prefix}.${classified_naming}#.fastq"
-    unclassified_naming = params.wf == "teton" ? "scrubbed" : "unclassified"
+    unclassified_naming = params.wf == "teton" || params.wf == "scrubber" ? "scrubbed" : "unclassified"
     unclassified = meta.single_end ? "${prefix}.${unclassified_naming}.fastq" : "${prefix}.${unclassified_naming}#.fastq"
     def is_tarball = db.getName().endsWith(".tar.gz") ? true : false
     """
@@ -67,9 +67,15 @@ process KRAKEN2 {
     fi
 
     if [ "$unclassified_naming" == "scrubbed" ]; then
+        # Rename scrubbed reads
+        if [ "$meta.single_end" == "false" ]; then
+            mv ${prefix}.${unclassified_naming}_1.fastq.gz ${prefix}_R1.scrubbed.fastq.gz
+            mv ${prefix}.${unclassified_naming}_2.fastq.gz ${prefix}_R2.scrubbed.fastq.gz
+        fi
+
         # Quick stats on reads
         zcat ${reads} | fastq-scan > original.json
-        zcat ${prefix}.scrubbed* | fastq-scan > scrubbed.json
+        zcat *.scrubbed.fastq.gz | fastq-scan > scrubbed.json
         scrubber-summary.py ${prefix} original.json scrubbed.json > ${prefix}.scrub.report.tsv
 
         # Remove host reads
diff --git a/modules/nf-core/kraken2/params-teton.json b/modules/nf-core/kraken2/params-teton.json
new file mode 100644
index 00000000..a43bd908
--- /dev/null
+++ b/modules/nf-core/kraken2/params-teton.json
@@ -0,0 +1,90 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/kraken2/params.json",
+    "title": "Kraken2 Module",
+    "description": "A module for taxonomic classification of sequence reads",
+    "type": "object",
+    "definitions": {
+        "kraken2_parameters": {
+            "title": "Scrubber (Kraken2) Parameters",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "fa_icon": "fas fa-exclamation-circle",
+            "properties": {
+                "quick_mode": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Quick operation (use first hit or hits)",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "confidence": {
+                    "type": "number",
+                    "default": 0.0,
+                    "description": "Confidence score threshold between 0 and 1",
+                    "fa_icon": "fas fa-expand-arrows-alt"
+                },
+                "minimum_base_quality": {
+                    "type": "integer",
+                    "default": 0,
+                    "description": "Minimum base quality used in classification",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "use_mpa_style": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Format report output like Kraken 1's kraken-mpa-report",
+                    "fa_icon": "fas fa-expand-arrows-alt"
+                },
+                "report_zero_counts": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Report counts for ALL taxa, even if counts are zero",
+                    "fa_icon": "fas fa-expand-arrows-alt"
+                },
+                "report_minimizer_data": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Include minimizer and distinct minimizer count information in report",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "use_names": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Print scientific names instead of just taxids",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "memory_mapping": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Avoid loading database into RAM",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "minimum_hit_groups": {
+                    "type": "integer",
+                    "default": 2,
+                    "description": "Minimum number of hit groups needed to make a call",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                },
+                "remove_filtered_reads": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Discard the classified and unclassified FASTQs prduced by Kraken2",
+                    "fa_icon": "fas fa-expand-arrows-alt",
+                    "hidden": true
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/kraken2_parameters"
+        }
+    ]
+}
diff --git a/modules/nf-core/kraken2/params.json b/modules/nf-core/kraken2/params.json
index 4b12e213..5dcccb94 100644
--- a/modules/nf-core/kraken2/params.json
+++ b/modules/nf-core/kraken2/params.json
@@ -81,7 +81,7 @@
                 "remove_filtered_reads": {
                     "type": "boolean",
                     "default": false,
-                    "description": "Discard the classified and unclassified FASTQs prduced by Kraken2",
+                    "description": "Discard the classified and unclassified FASTQs produced by Kraken2",
                     "fa_icon": "fas fa-expand-arrows-alt",
                     "hidden": true
                 }
diff --git a/modules/nf-core/sistr/main.nf b/modules/nf-core/sistr/main.nf
index b1ab7008..31cf0d82 100644
--- a/modules/nf-core/sistr/main.nf
+++ b/modules/nf-core/sistr/main.nf
@@ -13,8 +13,8 @@ process SISTR {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.2--pyhca03a8a_0' :
-        'quay.io/biocontainers/sistr_cmd:1.1.2--pyhca03a8a_0' }"
+        'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.2--pyhca03a8a_1' :
+        'quay.io/biocontainers/sistr_cmd:1.1.2--pyhca03a8a_1' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/subworkflows/local/abricate/test.yml b/subworkflows/local/abricate/test.yml
index 1b31f849..de9b9d6f 100644
--- a/subworkflows/local/abricate/test.yml
+++ b/subworkflows/local/abricate/test.yml
@@ -4,43 +4,43 @@
     - abricate
     - tools
   files:
-    - path: bactopia/bactopia-runs/abricate/merged-results/abricate.tsv
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/abricate.tsv
       contains: ['FILE', 'NUM_FOUND']
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.begin
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.err
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.log
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.out
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.run
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.begin
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.err
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.log
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.out
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.sh
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.sh
       contains: ['abricate', 'END_VERSIONS']
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/nf-merged-results.trace
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/nf-merged-results.trace
       contains: ['nextflow.trace']
-    - path: bactopia/bactopia-runs/abricate/merged-results/logs/abricate-concat/versions.yml
+    - path: bactopia/bactopia-runs/abricate-ncbi/merged-results/logs/abricate-concat/versions.yml
       contains: ['abricate']
-    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-dag.dot
+    - path: bactopia/bactopia-runs/abricate-ncbi/nf-reports/abricate-dag.dot
       contains: ['abricatedag', 'ABRICATE', 'versions']
-    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-report.html
+    - path: bactopia/bactopia-runs/abricate-ncbi/nf-reports/abricate-report.html
       contains: ['html', 'Nextflow', 'Report']
-    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-timeline.html
+    - path: bactopia/bactopia-runs/abricate-ncbi/nf-reports/abricate-timeline.html
       contains: ['html', 'Nextflow', 'timeline']
-    - path: bactopia/bactopia-runs/abricate/nf-reports/abricate-trace.txt
+    - path: bactopia/bactopia-runs/abricate-ncbi/nf-reports/abricate-trace.txt
       contains: ['task_id']
-    - path: bactopia/GCF_000292685/tools/abricate/GCF_000292685.txt
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/GCF_000292685.txt
       contains: ['FILE', 'COVERAGE', 'RESISTANCE']
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.begin
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.begin
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.err
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.err
       contains: ["database", "genes", "Done"]
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.log
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.log
       contains: ["database", "genes", "Done"]
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.out
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.out
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.run
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.sh
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.sh
       contains: ['abricate', 'END_VERSIONS']
-    - path: bactopia/GCF_000292685/tools/abricate/logs/nf-abricate.trace
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/nf-abricate.trace
       contains: ['nextflow.trace']
-    - path: bactopia/GCF_000292685/tools/abricate/logs/versions.yml
+    - path: bactopia/GCF_000292685/tools/abricate/ncbi/logs/versions.yml
       md5sum: 883068280465b2816cfae24f8ba0ec3c
diff --git a/subworkflows/local/abritamr/test.yml b/subworkflows/local/abritamr/test.yml
index be411857..f0c6ab53 100644
--- a/subworkflows/local/abritamr/test.yml
+++ b/subworkflows/local/abritamr/test.yml
@@ -29,7 +29,7 @@
     - path: bactopia/GCF_000292685/tools/abritamr/logs/nf-abritamr.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCF_000292685/tools/abritamr/logs/versions.yml
-      md5sum: 603690c9d9ad1d9cf8faa026765195d1
+      md5sum: 76491e13fdc40c767869c29792969379
     - path: bactopia/bactopia-runs/abritamr/nf-reports/abritamr-dag.dot
       contains: ['abritamr', 'ABRITAMR', 'versions']
     - path: bactopia/bactopia-runs/abritamr/nf-reports/abritamr-report.html
diff --git a/subworkflows/local/amrfinderplus/test.yml b/subworkflows/local/amrfinderplus/test.yml
index 21c73bb1..5789c3b6 100644
--- a/subworkflows/local/amrfinderplus/test.yml
+++ b/subworkflows/local/amrfinderplus/test.yml
@@ -61,4 +61,4 @@
     - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/nf-amrfinderplus.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCF_000292685/tools/amrfinderplus/logs/versions.yml
-      md5sum: 9933c8136bf5f0001ed5ec26405db0a7
+      md5sum: bc198f6b2e09d2ce26d1c9f77d60899a
diff --git a/subworkflows/local/ariba/test.yml b/subworkflows/local/ariba/test.yml
index 9736f11e..5baf6aae 100644
--- a/subworkflows/local/ariba/test.yml
+++ b/subworkflows/local/ariba/test.yml
@@ -4,41 +4,41 @@
     - ariba
     - bactopia-tools
   files:
-    - path: bactopia/bactopia-runs/ariba/merged-results/card-report.tsv
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/card-report.tsv
       contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
-    - path: bactopia/bactopia-runs/ariba/merged-results/card-summary.csv
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/card-summary.csv
       contains: ["name", "novel_var", "Clostridioides"]
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.begin
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.err
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.log
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.out
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.run
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.begin
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.err
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.log
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.out
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.sh
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.sh
       contains: ['csvtk', 'concat', "END_VERSIONS"]
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/nf-merged-results.trace
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/nf-merged-results.trace
       contains: ['nextflow.trace']
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-report/versions.yml
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-report/versions.yml
       md5sum: 344624d16fe24cfad6e9f45a19be708f
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.begin
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.err
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.log
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.out
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.run
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.begin
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.err
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.log
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.out
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.sh
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.sh
       contains: ['csvtk', 'concat', "END_VERSIONS"]
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/nf-merged-results.trace
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/nf-merged-results.trace
       contains: ['nextflow.trace']
-    - path: bactopia/bactopia-runs/ariba/merged-results/logs/card-summary/versions.yml
+    - path: bactopia/bactopia-runs/ariba-card/merged-results/logs/card-summary/versions.yml
       md5sum: 6551889c4545016b96a75751d9efdb38
-    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-dag.dot
+    - path: bactopia/bactopia-runs/ariba-card/nf-reports/ariba-dag.dot
       contains: ['aribadag', 'ARIBA', 'versions']
-    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-report.html
+    - path: bactopia/bactopia-runs/ariba-card/nf-reports/ariba-report.html
       contains: ['html', 'Nextflow', 'Report']
-    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-timeline.html
+    - path: bactopia/bactopia-runs/ariba-card/nf-reports/ariba-timeline.html
       contains: ['html', 'Nextflow', 'timeline']
-    - path: bactopia/bactopia-runs/ariba/nf-reports/ariba-trace.txt
+    - path: bactopia/bactopia-runs/ariba-card/nf-reports/ariba-trace.txt
       contains: ['task_id']
     - path: bactopia/SRR2838702/tools/ariba/card/SRR2838702-report.tsv
       contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
diff --git a/subworkflows/local/busco/main.nf b/subworkflows/local/busco/main.nf
index da0ba702..8563b9ff 100644
--- a/subworkflows/local/busco/main.nf
+++ b/subworkflows/local/busco/main.nf
@@ -13,7 +13,7 @@ options.args = [
     "--evalue ${params.busco_evalue}",
     "--limit ${params.busco_limit}"
 ].join(' ').replaceAll("\\s{2,}", " ").trim()
-options.subdir = params.run_name
+options.subdir = params.busco_lineage
 options.logs_use_prefix = true
 
 include { BUSCO as BUSCO_MODULE } from '../../../modules/nf-core/busco/main' addParams( options: options )
diff --git a/subworkflows/local/busco/test.yml b/subworkflows/local/busco/test.yml
index fd4c03e9..591049ee 100644
--- a/subworkflows/local/busco/test.yml
+++ b/subworkflows/local/busco/test.yml
@@ -4,30 +4,30 @@
     - busco
     - bactopia-tools
   files:
-    - path: bactopia/bactopia-runs/busco/merged-results/busco.tsv
-      md5sum: 15267d2162b35514e27bfca0a32b8e5c
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.begin
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.err
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.log
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.out
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.run
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/busco.tsv
+      md5sum: b5118703a4b6ef1274f9f894ebe2ed5c
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.begin
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.err
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.log
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.out
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.sh
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.sh
       contains: ['csvtk', 'END_VERSIONS']
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/nf-merged-results.trace
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/nf-merged-results.trace
       contains: ['nextflow.trace']
-    - path: bactopia/bactopia-runs/busco/merged-results/logs/busco-concat/versions.yml
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/merged-results/logs/busco-concat/versions.yml
       md5sum: b45e81d6e1c8a0b37a7b3ea491992002
-    - path: bactopia/bactopia-runs/busco/nf-reports/busco-dag.dot
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/nf-reports/busco-dag.dot
       contains: ['buscodag', 'BUSCO', 'versions']
-    - path: bactopia/bactopia-runs/busco/nf-reports/busco-report.html
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/nf-reports/busco-report.html
       contains: ['html', 'Nextflow', 'Report']
-    - path: bactopia/bactopia-runs/busco/nf-reports/busco-timeline.html
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/nf-reports/busco-timeline.html
       contains: ['html', 'Nextflow', 'timeline']
-    - path: bactopia/bactopia-runs/busco/nf-reports/busco-trace.txt
+    - path: bactopia/bactopia-runs/busco-bacteria_odb10/nf-reports/busco-trace.txt
       contains: ['task_id']
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/GCF_000292685-summary.txt
-      md5sum: 15267d2162b35514e27bfca0a32b8e5c
+      md5sum: b5118703a4b6ef1274f9f894ebe2ed5c
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/bbtools_err.log
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/bbtools_out.log
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/busco.log
@@ -56,41 +56,31 @@
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/prodigal_out.log
       md5sum: 50752acb1c5a20be886bfdfc06635bcb
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/logs/versions.yml
-      md5sum: fdd6b94718c21dd4c370acf841aafc92
+      md5sum: 79800901f8e3462158093c07bc2aeba9
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/.checkpoint
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/predicted.faa
-      md5sum: 8166471fc5f08c82fd5643ab42327f9d
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/predicted.fna
       md5sum: ddc508a18f60e7f3314534df50cdf8ca
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
-      md5sum: 8166471fc5f08c82fd5643ab42327f9d
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
       md5sum: ddc508a18f60e7f3314534df50cdf8ca
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/.bbtools_output/.checkpoint
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1272633at2.faa
-      md5sum: bc3d8e3ec26129fb17110134822fc8cd
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/fragmented_busco_sequences/1272633at2.fna
-      md5sum: c9d955773c7433464d5886d56c4cbf58
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1054741at2.faa
-      md5sum: a8f004eb3c63433eafe2e3886e680c85
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1054741at2.fna
-      md5sum: bb5835b69e7e09f1661a09b75df4887b
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.faa
-      md5sum: 85494768d2a27813a97e2e55e3e8424b
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/1132353at2.fna
-      md5sum: 955560ad0799a224a8e2c0ea033a91a7
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/961486at2.faa
-      md5sum: e70105bd9c0a92b6d442d9d48333e22a
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/busco_sequences/single_copy_busco_sequences/961486at2.fna
-      md5sum: 421d326188a45e6e0101a5448e200ba5
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/full_table.tsv
-      md5sum: c9651b88b10871abc260ee655898e828
+      contains: ["BUSCO", "Complete", "Fragmented", "Missing"]
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/.checkpoint
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/1054741at2.out
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/1132353at2.out
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/hmmer_output/961486at2.out
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/missing_busco_list.tsv
-      md5sum: 9939309df2da5419de88c32d1435c779
+      contains: ["BUSCO", "at2"]
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/short_summary.json
       contains: ["one_line_summary", "dataset"]
     - path: bactopia/GCF_000292685/tools/busco/bacteria_odb10/run_bacteria_odb10/short_summary.txt
diff --git a/subworkflows/local/gubbins/test.yml b/subworkflows/local/gubbins/test.yml
index b56ccf12..60ddef97 100644
--- a/subworkflows/local/gubbins/test.yml
+++ b/subworkflows/local/gubbins/test.yml
@@ -9,10 +9,10 @@
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.filtered_polymorphic_sites.phylip
       md5sum: 15efec56c27103e2f777d946a297d399
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.final_tree.tre
-      md5sum: e1a69691e9ca439db36d1544f482f403
+      contains: ["GCF_902713755", "GCF_000298385", "GCF_002849995", "GCF_000300075"]
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.masked.aln.gz
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.node_labelled.final_tree.tre
-      md5sum: accd0e5733897e53534c70dc24f8e74e
+      contains: ["GCF_902713755", "GCF_000298385", "GCF_002849995", "GCF_000300075"]
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.per_branch_statistics.csv
       md5sum: 2dc0dbae9a7cf545bfc56ac5d734342d
     - path: bactopia/bactopia-runs/gubbins/gubbins/gubbins.recombination_predictions.embl.gz
@@ -34,7 +34,7 @@
     - path: bactopia/bactopia-runs/gubbins/gubbins/logs/nf-gubbins.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/gubbins/gubbins/logs/versions.yml
-      md5sum: 0720185e5a55ffba81a6fd4828be73ee
+      md5sum: 9ddc482d1d3ed3782ea8fecf9db5306c
     - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-dag.dot
       contains: ['gubbinsdag', 'GUBBINS', 'versions']
     - path: bactopia/bactopia-runs/gubbins/nf-reports/gubbins-report.html
diff --git a/subworkflows/local/k2scrubber/main.nf b/subworkflows/local/k2scrubber/main.nf
new file mode 100644
index 00000000..216d309b
--- /dev/null
+++ b/subworkflows/local/k2scrubber/main.nf
@@ -0,0 +1,50 @@
+//
+// k2scrubber - Scrub human reads from FASTQ files using Kraken2 and human pangenome reference
+//
+
+include { initOptions } from '../../../lib/nf/functions'
+
+// HPRC download options
+wget_opts = initOptions(params.containsKey("options") ? params.options : [:], 'wget')
+wget_opts.args = [
+    params.no_check_certificate ? "--no-check-certificate" : "",
+    "-O k2_HPRC_20230810.tar.gz",
+    "https://zenodo.org/records/8339732/files/k2_HPRC_20230810.tar.gz?download=1",
+].join(' ').replaceAll("\\s{2,}", " ").trim()
+wget_opts.args2 = "k2_HPRC_20230810.tar.gz"
+
+// Kraken2 Options
+k2_options = initOptions(params.containsKey("options") ? params.options : [:], 'kraken2')
+k2_options.args = [
+    params.quick_mode ? "--quick" : "",
+    params.use_mpa_style ? "--use-mpa-style" : "",
+    params.report_zero_counts ? "--report-zero-counts" : "",
+    params.report_minimizer_data ? "--report-minimizer-data" : "",
+    params.use_names ? "--use-names" : "",
+    params.memory_mapping ? "--memory-mapping" : "",
+    "--confidence ${params.confidence}",
+    "--minimum-hit-groups ${params.minimum_hit_groups}",
+    "--minimum-base-quality ${params.minimum_base_quality}"
+].join(' ').replaceAll("\\s{2,}", " ").trim()
+
+include { CUSTOM_WGET as WGET_HPRC } from '../../../modules/nf-core/custom/wget/main' addParams( options: wget_opts )
+include { KRAKEN2 } from '../../../modules/nf-core/kraken2/main' addParams( options: k2_options )
+
+workflow K2SCRUBBER {
+    take:
+    reads // channel: [ val(meta), [ fasta ] ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    WGET_HPRC()
+    KRAKEN2(reads, WGET_HPRC.out.download)
+    ch_versions = ch_versions.mix(KRAKEN2.out.versions)
+
+    emit:
+    scrubbed = KRAKEN2.out.unclassified
+    human = KRAKEN2.out.classified
+    kraken2_report = KRAKEN2.out.kraken2_report
+    scrub_report = KRAKEN2.out.scrub_report
+    versions = ch_versions // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/k2scrubber/meta.yml b/subworkflows/local/k2scrubber/meta.yml
new file mode 100644
index 00000000..59369c13
--- /dev/null
+++ b/subworkflows/local/k2scrubber/meta.yml
@@ -0,0 +1,51 @@
+name: k2scrubber
+description: Scrub human reads from FASTQ files using Kraken2 and human pangenome reference
+icon: false
+keywords:
+  - TAGS
+modules:
+  - LIST_OF_MODULES
+input:
+  - meta:
+    type: map
+    description: |
+      Groovy Map containing sample information
+      e.g. [ id:'test', single_end:false ]
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+docs:
+  meta:
+    title: k2scrubber
+    description: >
+      A Bactopia Tool which uses...
+  introduction: |
+      The `k2scrubber` module uses...
+  output:
+    tree: |
+
+    add_note: false
+    folders:
+      - name: Top Level
+        description: |
+          Below are results that are in the base directory.
+        table: |
+          | Filename    | Description |
+          |-------------|-------------|
+          |  |  |
+      - name: k2scrubber
+        description: |
+          Below is a description of the _per-sample_ results from [k2scrubber](SUBWORKFLOW_LINK).
+        table: |
+          | Filename              | Description |
+          |-----------------------|-------------|
+          |  |  |
+  citations:
+    - add to citations.yml
diff --git a/subworkflows/local/k2scrubber/test.nf b/subworkflows/local/k2scrubber/test.nf
new file mode 100644
index 00000000..0d4cde8b
--- /dev/null
+++ b/subworkflows/local/k2scrubber/test.nf
@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { K2SCRUBBER } from './main.nf' 
+
+workflow test_k2scrubber {
+
+    inputs = tuple( )
+
+    K2SCRUBBER ( inputs )
+}
+
+
+include { SCRUBBER } from './main.nf' addParams(scrubber_db: params.test_data['datasets']['scrubber'])
+
+workflow test_scrubber_pe {
+
+    inputs = tuple(
+        [ id:"SRR2838702", single_end:false ],
+        [file(params.test_data['species']['portiera']['illumina']['r1'], checkIfExists: true),
+         file(params.test_data['species']['portiera']['illumina']['r2'], checkIfExists: true)]
+    )
+
+    SCRUBBER ( inputs )
+}
+
+workflow test_scrubber_se {
+
+    inputs = tuple(
+        [ id:"SRR2838702", single_end:true ],
+        [file(params.test_data['species']['portiera']['illumina']['se'], checkIfExists: true)]
+    )
+
+    SCRUBBER ( inputs )
+}
diff --git a/subworkflows/local/k2scrubber/test.yml b/subworkflows/local/k2scrubber/test.yml
new file mode 100644
index 00000000..e5657549
--- /dev/null
+++ b/subworkflows/local/k2scrubber/test.yml
@@ -0,0 +1,64 @@
+- name: k2scrubber-test-pe
+  command: bash -c 'nextflow run ./subworkflows/local/scrubber/test.nf -entry test_scrubber_pe --wf scrubber -c nextflow.config ${BACTOPIA_ARGS}'
+  tags:
+    - k2scrubber
+    - bactopia-tools
+  files:
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
+      contains: ['scrubberdag', 'scrubber', 'versions']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
+      contains: ['html', 'Nextflow', 'Report']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
+      contains: ['html', 'Nextflow', 'timeline']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
+      contains: ['task_id']
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702_R1.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702_R2.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.begin
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.err
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.log
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.out
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.run
+      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.sh
+      contains: ['scrub', 'END_VERSIONS']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.trace
+      contains: ['nextflow.trace']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/versions.yml
+      md5sum: 9223d0f9690923042b457b010e88d45c
+
+- name: k2scrubber-test-se
+  command: bash -c 'nextflow run ./subworkflows/local/scrubber/test.nf -entry test_scrubber_se --wf scrubber -c nextflow.config ${BACTOPIA_ARGS}'
+  tags:
+    - k2scrubber
+    - bactopia-tools
+  files:
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
+      contains: ['scrubberdag', 'scrubber', 'versions']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
+      contains: ['html', 'Nextflow', 'Report']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
+      contains: ['html', 'Nextflow', 'timeline']
+    - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
+      contains: ['task_id']
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.begin
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.err
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.log
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.out
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.run
+      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.sh
+      contains: ['scrub', 'END_VERSIONS']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.trace
+      contains: ['nextflow.trace']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/versions.yml
+      md5sum: 2feea5bb3fda5f9fe18d461b430ac276
diff --git a/subworkflows/local/panaroo/test.yml b/subworkflows/local/panaroo/test.yml
index 8eebb9ea..8b2a19b4 100644
--- a/subworkflows/local/panaroo/test.yml
+++ b/subworkflows/local/panaroo/test.yml
@@ -58,9 +58,9 @@
     - path: bactopia/bactopia-runs/panaroo/panaroo/logs/nf-panaroo.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/panaroo/panaroo/logs/versions.yml
-      md5sum: b43b05d590ef8086ccc4cd7f5040d4d0
+      md5sum: 52678674115cb226f088d2cde569b8c9
     - path: bactopia/bactopia-runs/panaroo/panaroo/pan_genome_reference.fa
-      md5sum: d0b03cdfaab8965d86cb1045db3c2d20
+      contains: ["dnaK", "nuoN", "glyQ"]
     - path: bactopia/bactopia-runs/panaroo/panaroo/pre_filt_graph.gml
       contains: ["lengths", "graph", "node"]
     - path: bactopia/bactopia-runs/panaroo/panaroo/struct_presence_absence.Rtab
diff --git a/subworkflows/local/plasmidfinder/test.yml b/subworkflows/local/plasmidfinder/test.yml
index 2ca85ff3..2351aabc 100644
--- a/subworkflows/local/plasmidfinder/test.yml
+++ b/subworkflows/local/plasmidfinder/test.yml
@@ -18,7 +18,7 @@
     - path: bactopia/bactopia-runs/plasmidfinder/merged-results/logs/plasmidfinder-concat/versions.yml
       contains: ['csvtk']
     - path: bactopia/bactopia-runs/plasmidfinder/merged-results/plasmidfinder.tsv
-      md5sum: 7aa17dc82d1efd058422d8e0cc45db1a
+      contains: ['Sample', 'GCF_000017085', 'aureus']
     - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-dag.dot
       contains: ['plasmidfinderdag', 'PLASMIDFINDER', 'versions']
     - path: bactopia/bactopia-runs/plasmidfinder/nf-reports/plasmidfinder-report.html
@@ -34,7 +34,7 @@
     - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.json
       contains: ["plasmidfinder", "results", "RepA", "GCF_000017085"]
     - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.tsv
-      md5sum: 7aa17dc82d1efd058422d8e0cc45db1a
+      contains: ['Sample', 'GCF_000017085', 'aureus']
     - path: bactopia/GCF_000017085/tools/plasmidfinder/GCF_000017085.txt
       contains: ['Results', 'Plasmid', 'Query', 'template']
     - path: bactopia/GCF_000017085/tools/plasmidfinder/logs/nf-plasmidfinder.begin
diff --git a/subworkflows/local/scrubber/test.yml b/subworkflows/local/scrubber/test.yml
index 5349942b..597f8aba 100644
--- a/subworkflows/local/scrubber/test.yml
+++ b/subworkflows/local/scrubber/test.yml
@@ -5,31 +5,31 @@
     - bactopia-tools
   files:
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
-      contains: ['scrubberdag', 'SRAHUMANSCRUBBER', 'versions']
+      contains: ['scrubberdag', 'scrubber', 'versions']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
       contains: ['html', 'Nextflow', 'Report']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
       contains: ['html', 'Nextflow', 'timeline']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
       contains: ['task_id']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702_R1.scrubbed.fastq.gz
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702_R2.scrubbed.fastq.gz
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.begin
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702_R1.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702_R2.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.begin
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.err
-      contains: ['aligns_to', 'FastaReader', 'total']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.log
-      contains: ['aligns_to', 'FastaReader', 'total']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.out
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.err
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.log
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.out
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.run
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.sh
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.sh
       contains: ['scrub', 'END_VERSIONS']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.trace
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.trace
       contains: ['nextflow.trace']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/versions.yml
-      md5sum: 6964d293234668d561237412de067eec
+    - path: bactopia/SRR2838702/tools/scrubber/logs/versions.yml
+      md5sum: 9223d0f9690923042b457b010e88d45c
 
 - name: scrubber-test-se
   command: bash -c 'nextflow run ./subworkflows/local/scrubber/test.nf -entry test_scrubber_se --wf scrubber -c nextflow.config ${BACTOPIA_ARGS}'
@@ -38,27 +38,27 @@
     - bactopia-tools
   files:
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-dag.dot
-      contains: ['scrubberdag', 'SRAHUMANSCRUBBER', 'versions']
+      contains: ['scrubberdag', 'scrubber', 'versions']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-report.html
       contains: ['html', 'Nextflow', 'Report']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-timeline.html
       contains: ['html', 'Nextflow', 'timeline']
     - path: bactopia/bactopia-runs/scrubber/nf-reports/scrubber-trace.txt
       contains: ['task_id']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/SRR2838702.scrubbed.fastq.gz
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.begin
+    - path: bactopia/SRR2838702/tools/scrubber/SRR2838702.scrubbed.fastq.gz
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.begin
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.err
-      contains: ['aligns_to', 'FastaReader', 'total']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.log
-      contains: ['aligns_to', 'FastaReader', 'total']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.out
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.err
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.log
+      contains: ['Loading', 'classified', 'unclassified']
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.out
       md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.run
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.run
       contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.sh
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.sh
       contains: ['scrub', 'END_VERSIONS']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/nf-srahumanscrubber.trace
+    - path: bactopia/SRR2838702/tools/scrubber/logs/nf-scrubber.trace
       contains: ['nextflow.trace']
-    - path: bactopia/SRR2838702/tools/srahumanscrubber/logs/versions.yml
-      md5sum: 7f879dc589c9f00beaf3551c06cc0b95
+    - path: bactopia/SRR2838702/tools/scrubber/logs/versions.yml
+      md5sum: 2feea5bb3fda5f9fe18d461b430ac276
diff --git a/subworkflows/local/sistr/test.yml b/subworkflows/local/sistr/test.yml
index 544883d0..db9817e3 100644
--- a/subworkflows/local/sistr/test.yml
+++ b/subworkflows/local/sistr/test.yml
@@ -45,4 +45,4 @@
     - path: bactopia/GCF_016028495/tools/sistr/logs/nf-sistr.trace
       contains: ['nextflow.trace']
     - path: bactopia/GCF_016028495/tools/sistr/logs/versions.yml
-      md5sum: 9ce214ed7a2ba7b43b59e3a87553fccc
+      md5sum: 92799fc66ab9a577152eeb7e2186bc7e
diff --git a/subworkflows/local/snippy/test.yml b/subworkflows/local/snippy/test.yml
index cbaab5f4..60b0f439 100644
--- a/subworkflows/local/snippy/test.yml
+++ b/subworkflows/local/snippy/test.yml
@@ -35,7 +35,7 @@
     - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/snippy/gubbins/logs/versions.yml
-      md5sum: 06e837b60e52d63b0f5b53d25f63924d
+      md5sum: f4bc8f0efac4a9d957a06ac5efb2853c
     - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.alninfo
       md5sum: b0fba4469a915df9872ca077eb2cf808
     - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.bionj
@@ -98,7 +98,7 @@
     - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/snippy/snippy-core/logs/versions.yml
-      md5sum: 0362757dde048c5c4f118e8ec2256330
+      md5sum: d491166dddb81e68df7da2e8a8695985
     - path: bactopia/bactopia-runs/snippy/snpdists/core-snp.distance.tsv
       md5sum: eca1078f443287c1bfdac84cdbce50b5
     - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.begin
@@ -133,7 +133,7 @@
     - path: bactopia/test0/tools/snippy/snippy/logs/test0.log
       contains: ["snippy", "snpEff", "test0", "consensus"]
     - path: bactopia/test0/tools/snippy/snippy/logs/versions.yml
-      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
+      md5sum: 83e1315aaa8e45a6fc36e669334f22d6
     - path: bactopia/test0/tools/snippy/snippy/test0.aligned.fa.gz
     - path: bactopia/test0/tools/snippy/snippy/test0.annotated.vcf.gz
     - path: bactopia/test0/tools/snippy/snippy/test0.bam
@@ -171,7 +171,7 @@
     - path: bactopia/test1/tools/snippy/snippy/logs/test1.log
       contains: ["snippy", "snpEff", "test1", "consensus"]
     - path: bactopia/test1/tools/snippy/snippy/logs/versions.yml
-      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
+      md5sum: 83e1315aaa8e45a6fc36e669334f22d6
     - path: bactopia/test1/tools/snippy/snippy/test1.aligned.fa.gz
     - path: bactopia/test1/tools/snippy/snippy/test1.annotated.vcf.gz
     - path: bactopia/test1/tools/snippy/snippy/test1.bam
@@ -209,7 +209,7 @@
     - path: bactopia/test2/tools/snippy/snippy/logs/test2.log
       contains: ["snippy", "snpEff", "test2", "consensus"]
     - path: bactopia/test2/tools/snippy/snippy/logs/versions.yml
-      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
+      md5sum: 83e1315aaa8e45a6fc36e669334f22d6
     - path: bactopia/test2/tools/snippy/snippy/test2.aligned.fa.gz
     - path: bactopia/test2/tools/snippy/snippy/test2.annotated.vcf.gz
     - path: bactopia/test2/tools/snippy/snippy/test2.bam
@@ -247,7 +247,7 @@
     - path: bactopia/test3/tools/snippy/snippy/logs/test3.log
       contains: ["snippy", "snpEff", "test3", "consensus"]
     - path: bactopia/test3/tools/snippy/snippy/logs/versions.yml
-      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
+      md5sum: 83e1315aaa8e45a6fc36e669334f22d6
     - path: bactopia/test3/tools/snippy/snippy/test3.aligned.fa.gz
     - path: bactopia/test3/tools/snippy/snippy/test3.annotated.vcf.gz
     - path: bactopia/test3/tools/snippy/snippy/test3.bam
@@ -285,7 +285,7 @@
     - path: bactopia/test4/tools/snippy/snippy/logs/test4.log
       contains: ["snippy", "snpEff", "test4", "consensus"]
     - path: bactopia/test4/tools/snippy/snippy/logs/versions.yml
-      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
+      md5sum: 83e1315aaa8e45a6fc36e669334f22d6
     - path: bactopia/test4/tools/snippy/snippy/test4.aligned.fa.gz
     - path: bactopia/test4/tools/snippy/snippy/test4.annotated.vcf.gz
     - path: bactopia/test4/tools/snippy/snippy/test4.bam
@@ -345,7 +345,7 @@
     - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/snippy/gubbins/logs/versions.yml
-      md5sum: e763a9a67609a03acd4dfec3e2071234
+      md5sum: dc520752b4284352ee7e847a0eba8afc
     - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.alninfo
       md5sum: 3538bdd4729b861eb66eb3e69060812d
     - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.bionj
@@ -408,7 +408,7 @@
     - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.trace
       contains: ['nextflow.trace']
     - path: bactopia/bactopia-runs/snippy/snippy-core/logs/versions.yml
-      md5sum: 02f01df9b4b6a6be837acbc9bced050a
+      md5sum: db38179edfe377c5d2f5b325e1d32357
     - path: bactopia/bactopia-runs/snippy/snpdists/core-snp.distance.tsv
       md5sum: eca1078f443287c1bfdac84cdbce50b5
     - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.begin
@@ -443,7 +443,7 @@
     - path: bactopia/test0/tools/snippy/snippy/logs/test0.log
       contains: ["snippy", "snpEff", "test0", "consensus"]
     - path: bactopia/test0/tools/snippy/snippy/logs/versions.yml
-      md5sum: 90cc2953b8258a258cbdf45e82689115
+      md5sum: 06a418bccf2e26153a11324f523cd2ab
     - path: bactopia/test0/tools/snippy/snippy/test0.aligned.fa.gz
     - path: bactopia/test0/tools/snippy/snippy/test0.annotated.vcf.gz
     - path: bactopia/test0/tools/snippy/snippy/test0.bam
@@ -481,7 +481,7 @@
     - path: bactopia/test1/tools/snippy/snippy/logs/test1.log
       contains: ["snippy", "snpEff", "test1", "consensus"]
     - path: bactopia/test1/tools/snippy/snippy/logs/versions.yml
-      md5sum: 90cc2953b8258a258cbdf45e82689115
+      md5sum: 06a418bccf2e26153a11324f523cd2ab
     - path: bactopia/test1/tools/snippy/snippy/test1.aligned.fa.gz
     - path: bactopia/test1/tools/snippy/snippy/test1.annotated.vcf.gz
     - path: bactopia/test1/tools/snippy/snippy/test1.bam
@@ -519,7 +519,7 @@
     - path: bactopia/test2/tools/snippy/snippy/logs/test2.log
       contains: ["snippy", "snpEff", "test2", "consensus"]
     - path: bactopia/test2/tools/snippy/snippy/logs/versions.yml
-      md5sum: 90cc2953b8258a258cbdf45e82689115
+      md5sum: 06a418bccf2e26153a11324f523cd2ab
     - path: bactopia/test2/tools/snippy/snippy/test2.aligned.fa.gz
     - path: bactopia/test2/tools/snippy/snippy/test2.annotated.vcf.gz
     - path: bactopia/test2/tools/snippy/snippy/test2.bam
@@ -557,7 +557,7 @@
     - path: bactopia/test3/tools/snippy/snippy/logs/test3.log
       contains: ["snippy", "snpEff", "test3", "consensus"]
     - path: bactopia/test3/tools/snippy/snippy/logs/versions.yml
-      md5sum: 90cc2953b8258a258cbdf45e82689115
+      md5sum: 06a418bccf2e26153a11324f523cd2ab
     - path: bactopia/test3/tools/snippy/snippy/test3.aligned.fa.gz
     - path: bactopia/test3/tools/snippy/snippy/test3.annotated.vcf.gz
     - path: bactopia/test3/tools/snippy/snippy/test3.bam
@@ -595,7 +595,7 @@
     - path: bactopia/test4/tools/snippy/snippy/logs/test4.log
       contains: ["snippy", "snpEff", "test4", "consensus"]
     - path: bactopia/test4/tools/snippy/snippy/logs/versions.yml
-      md5sum: 90cc2953b8258a258cbdf45e82689115
+      md5sum: 06a418bccf2e26153a11324f523cd2ab
     - path: bactopia/test4/tools/snippy/snippy/test4.aligned.fa.gz
     - path: bactopia/test4/tools/snippy/snippy/test4.annotated.vcf.gz
     - path: bactopia/test4/tools/snippy/snippy/test4.bam
diff --git a/subworkflows/local/srahumanscrubber/main.nf b/subworkflows/local/srahumanscrubber/main.nf
new file mode 100644
index 00000000..8b9013f9
--- /dev/null
+++ b/subworkflows/local/srahumanscrubber/main.nf
@@ -0,0 +1,35 @@
+//
+// srahumanscrubber - Scrub human reads from FASTQ files using SRA Human Scrubber
+//
+
+include { initOptions } from '../../../lib/nf/functions'
+options = initOptions(params.containsKey("options") ? params.options : [:], 'srahumanscrubber')
+options.is_module = params.wf == 'scrubber' ? true : false
+options.args = ""
+options.ignore = [".db"]
+
+include { SRAHUMANSCRUBBER_INITDB } from '../../../modules/nf-core/srahumanscrubber/initdb/main' addParams( )
+
+if (params.wf == 'teton') {
+    include { SRAHUMANSCRUBBER_SCRUB_TETON as SRAHUMANSCRUBBER_SCRUB } from '../../../modules/nf-core/srahumanscrubber/scrub/main' addParams( options: options )
+} else if (params.wf == 'cleanyerreads') {
+    include { SRAHUMANSCRUBBER_SCRUB_MAIN as SRAHUMANSCRUBBER_SCRUB } from '../../../modules/nf-core/srahumanscrubber/scrub/main' addParams( options: options )
+} else {
+    include { SRAHUMANSCRUBBER_SCRUB } from '../../../modules/nf-core/srahumanscrubber/scrub/main' addParams( options: options )
+}
+
+workflow SCRUBBER {
+    take:
+    reads // channel: [ val(meta), [ reads ] ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    SRAHUMANSCRUBBER_INITDB()
+    SRAHUMANSCRUBBER_SCRUB(reads, SRAHUMANSCRUBBER_INITDB.out.db)
+    ch_versions = ch_versions.mix(SRAHUMANSCRUBBER_SCRUB.out.versions.first())
+
+    emit:
+    scrubbed = SRAHUMANSCRUBBER_SCRUB.out.scrubbed
+    versions = ch_versions // channel: [ versions.yml ]
+}
diff --git a/subworkflows/local/srahumanscrubber/meta.yml b/subworkflows/local/srahumanscrubber/meta.yml
new file mode 100644
index 00000000..5d0db579
--- /dev/null
+++ b/subworkflows/local/srahumanscrubber/meta.yml
@@ -0,0 +1,51 @@
+name: srahumanscrubber
+description: Scrub human reads from FASTQ files using SRA Human Scrubber
+icon: false
+keywords:
+  - TAGS
+modules:
+  - LIST_OF_MODULES
+input:
+  - meta:
+    type: map
+    description: |
+      Groovy Map containing sample information
+      e.g. [ id:'test', single_end:false ]
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+docs:
+  meta:
+    title: srahumanscrubber
+    description: >
+      A Bactopia Tool which uses...
+  introduction: |
+      The `srahumanscrubber` module uses...
+  output:
+    tree: |
+
+    add_note: false
+    folders:
+      - name: Top Level
+        description: |
+          Below are results that are in the base directory.
+        table: |
+          | Filename    | Description |
+          |-------------|-------------|
+          |  |  |
+      - name: srahumanscrubber
+        description: |
+          Below is a description of the _per-sample_ results from [srahumanscrubber](SUBWORKFLOW_LINK).
+        table: |
+          | Filename              | Description |
+          |-----------------------|-------------|
+          |  |  |
+  citations:
+    - add to citations.yml
diff --git a/subworkflows/local/srahumanscrubber/test.nf b/subworkflows/local/srahumanscrubber/test.nf
new file mode 100644
index 00000000..d51fee69
--- /dev/null
+++ b/subworkflows/local/srahumanscrubber/test.nf
@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+include { SRAHUMANSCRUBBER } from './main.nf' 
+
+workflow test_srahumanscrubber {
+
+    inputs = tuple( )
+
+    SRAHUMANSCRUBBER ( inputs )
+}
diff --git a/subworkflows/local/srahumanscrubber/test.yml b/subworkflows/local/srahumanscrubber/test.yml
new file mode 100644
index 00000000..178551ba
--- /dev/null
+++ b/subworkflows/local/srahumanscrubber/test.yml
@@ -0,0 +1,10 @@
+- name: srahumanscrubber-test
+  command: bash -c 'nextflow run ./subworkflows/local/srahumanscrubber/test.nf -entry test_srahumanscrubber --wf srahumanscrubber -c nextflow.config ${BACTOPIA_ARGS}'
+  tags:
+    - srahumanscrubber
+    - bactopia-tools
+  files:
+    - path: OUTPUTFILE
+      contains: ['TEXT_A', 'TEXT_B']
+    - path: OUTPUTFILE
+      md5sum: a1000000000000000000000000000000