diff --git a/modules/nf-core/vrhyme/extractunbinned/main.nf b/modules/nf-core/vrhyme/extractunbinned/main.nf
index 0050bb3066d6..7da7e3cfe330 100644
--- a/modules/nf-core/vrhyme/extractunbinned/main.nf
+++ b/modules/nf-core/vrhyme/extractunbinned/main.nf
@@ -9,25 +9,33 @@ process VRHYME_EXTRACTUNBINNED {
 
     input:
     tuple val(meta), path(membership)
-    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta)
 
     output:
-    tuple val(meta), path("*_unbinned_sequences.fasta") , emit: unbinned_sequences
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("${prefix}.fasta") , emit: unbinned_sequences
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString().replaceAll(/\.gz$/, '')
+    def gunzip      = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${fasta_input}" : ""
+    def cleanup     = fasta.getExtension() == "gz" ? "rm ${fasta_input}" : ""
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
+    ${gunzip}
+
     extract_unbinned_sequences.py \\
         -i $membership \\
-        -f $fasta \\
-        -o ${prefix}_unbinned_sequences.fasta \\
+        -f $fasta_input \\
+        -o ${prefix}.fasta \\
         $args
 
+    ${cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vrhyme: \$(echo \$(vRhyme --version 2>&1) | sed 's/^.*vRhyme v//; s/Using.*\$//' )
@@ -35,10 +43,11 @@ process VRHYME_EXTRACTUNBINNED {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}_unbinned_sequences"
+    def fasta_input = fasta.toString() - ~/\.gz$/
+    if( "$fasta_input" == "${prefix}.fasta" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
-    touch ${prefix}_unbinned_sequences.fasta
+    touch ${prefix}.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml
index c9a9b941d595..416798f1add1 100644
--- a/modules/nf-core/vrhyme/extractunbinned/meta.yml
+++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml
@@ -22,21 +22,25 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - membership:
         type: file
         description: TSV file containing information regarding which bins input sequences
           were placed information
         pattern: "*.{tsv}"
-  - - meta:
+        ontologies:
+          - edam: http://edamontology.org/format_3475 # TSV
+  - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing information related to the fasta
+          e.g. [ id:'test' ]
     - fasta:
         type: file
         description: FASTA file containing contigs/scaffolds input into vRhyme
-        pattern: "*.{fasta,fna,fa}"
+        pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   - unbinned_sequences:
       - meta:
@@ -44,10 +48,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*_unbinned_sequences.fasta":
+      - "${prefix}.fasta":
           type: file
           description: FASTA file containing unbinned sequences
           pattern: "*_unbinned_sequences.fasta"
+          ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test
new file mode 100644
index 000000000000..4899735b029f
--- /dev/null
+++ b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test
@@ -0,0 +1,79 @@
+nextflow_process {
+
+    name "Test Process VRHYME_EXTRACTUNBINNED"
+
+    script "../main.nf"
+    process "VRHYME_EXTRACTUNBINNED"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/extractunbinned"
+
+    setup {
+
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                ]
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+    }
+
+    test("test_vrhyme_extractunbinned") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_extractunbinned -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.membership
+                input[1] = [
+                    [id:'test',single_end:false],// meta map
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap
new file mode 100644
index 000000000000..110efdc2b26d
--- /dev/null
+++ b/modules/nf-core/vrhyme/extractunbinned/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test_vrhyme_extractunbinned -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-30T20:31:33.979555851"
+    },
+    "test_vrhyme_extractunbinned": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ],
+                "unbinned_sequences": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_unbinned_sequences.fasta:md5,816e986c8ad8f277eb4a4891a12d7aff"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,19f257878bced6c770eaf8ed45151b96"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T10:00:14.099653894"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml
index 1302b2ea24fe..ccbb1a401acd 100644
--- a/modules/nf-core/vrhyme/linkbins/meta.yml
+++ b/modules/nf-core/vrhyme/linkbins/meta.yml
@@ -22,7 +22,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - bins:
         type: directory
         description: Directory file containing bin FASTA files output by vRhyme (each
@@ -38,11 +38,14 @@ output:
           type: file
           description: FASTA file containing all bins that have been linked by N's
           pattern: "*_linked_bins.fasta"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@CarsonJM"
 maintainers:
diff --git a/modules/nf-core/vrhyme/linkbins/tests/main.nf.test b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test
new file mode 100644
index 000000000000..36936f018c17
--- /dev/null
+++ b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test
@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process VRHYME_LINKBINS"
+
+    script "../main.nf"
+    process "VRHYME_LINKBINS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vrhyme"
+    tag "vrhyme/vrhyme"
+    tag "vrhyme/linkbins"
+
+    setup {
+        run("VRHYME_VRHYME") {
+            script "../../vrhyme/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
+                    ]
+                    ]
+				input[1] = [
+				    [ id:'test' ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
+                """
+            }
+        }
+    }
+
+    test("vrhyme_linkbins") {
+
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("test_vrhyme_linkbins -- stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = VRHYME_VRHYME.out.bins
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap
new file mode 100644
index 000000000000..2ca129f165ca
--- /dev/null
+++ b/modules/nf-core/vrhyme/linkbins/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "vrhyme_linkbins": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,92cee5d85211d1e657f67ba75d3b2b30"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ],
+                "linked_bins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,92cee5d85211d1e657f67ba75d3b2b30"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T14:18:15.131038697"
+    },
+    "test_vrhyme_linkbins -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ],
+                "linked_bins": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_linked_bins.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3e9001733bcdf459aafc8786cce5c4ca"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T14:18:32.716327779"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vrhyme/vrhyme/main.nf b/modules/nf-core/vrhyme/vrhyme/main.nf
index 65be074ac8cd..a65788613816 100644
--- a/modules/nf-core/vrhyme/vrhyme/main.nf
+++ b/modules/nf-core/vrhyme/vrhyme/main.nf
@@ -9,7 +9,7 @@ process VRHYME_VRHYME {
 
     input:
     tuple val(meta), path(reads)
-    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta)
 
     output:
     tuple val(meta), path("vRhyme_best_bins_fasta/")                , emit: bins
@@ -23,9 +23,14 @@ process VRHYME_VRHYME {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def fasta_input = fasta.toString().replaceAll(/\.gz$/, '')
+    def gunzip      = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${fasta_input}" : ""
+    def cleanup     = fasta.getExtension() == "gz" ? "rm ${fasta_input}" : ""
     """
+    ${gunzip}
+
     vRhyme \\
-        -i $fasta \\
+        -i $fasta_input \\
         -r $reads \\
         -o $prefix \\
         -t $task.cpus \\
@@ -33,6 +38,8 @@ process VRHYME_VRHYME {
 
     mv $prefix/vRhyme_best_bins_fasta/ vRhyme_best_bins_fasta
 
+    ${cleanup}
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         vrhyme: \$(echo \$(vRhyme --version 2>&1) | sed 's/^.*vRhyme v//; s/Using.*\$//' ))
@@ -40,7 +47,6 @@ process VRHYME_VRHYME {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p $prefix
diff --git a/modules/nf-core/vrhyme/vrhyme/meta.yml b/modules/nf-core/vrhyme/vrhyme/meta.yml
index e020a1acde04..b76810fbc4dc 100644
--- a/modules/nf-core/vrhyme/vrhyme/meta.yml
+++ b/modules/nf-core/vrhyme/vrhyme/meta.yml
@@ -22,27 +22,31 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test']
     - reads:
         type: file
         description: Preprocessed FASTQ file containing sample reads
         pattern: "*.{fastq}"
-  - - meta:
+        ontologies:
+          - edam: http://edamontology.org/format_1930 # FASTQ
+  - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing fasta information
+          e.g. [ id:'test']
     - fasta:
         type: file
         description: Contigs/scaffolds identified as viral
-        pattern: "*.{fna,fasta,fa}"
+        pattern: "*.{fna,fasta,fa,fasta.gz,fa.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
 output:
   - bins:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - vRhyme_best_bins_fasta/:
           type: directory
           description: Directory containing bin FASTA files
@@ -52,11 +56,13 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test']
       - "**/vRhyme_best_bins.*.membership.tsv":
           type: file
           description: TSV file describing the contig/scaffold membership of each bin
           pattern: "vRhyme_best_bins.*.membership.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
   - summary:
       - meta:
           type: map
@@ -67,11 +73,13 @@ output:
           type: file
           description: TSV file summarizing the attributes of each bin
           pattern: "vRhyme_best_bins.*.summary.tsv"
+          ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: []
 authors:
   - "@CarsonJM"
 maintainers:
diff --git a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
index 5ff7f4e2dc98..57af398ec47d 100644
--- a/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
+++ b/modules/nf-core/vrhyme/vrhyme/tests/main.nf.test
@@ -10,22 +10,6 @@ nextflow_process {
     tag "modules_vrhyme"
     tag "vrhyme"
     tag "vrhyme/vrhyme"
-    tag "gunzip"
-
-    setup {
-        run("GUNZIP") {
-            script "../../../gunzip/main.nf"
-            process {
-                """
-                input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
-				]
-
-                """
-            }
-        }
-    }
 
     test("test-vrhyme-vrhyme") {
 
@@ -33,14 +17,16 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    [
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
 				    ]
 				]
-				input[1] = GUNZIP.out.gunzip
-
+				input[1] = [
+				    [ id:'test', single_end:false ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
                 """
             }
         }
@@ -65,14 +51,16 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ],
 				    [
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz', checkIfExists: true),
 				        file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz', checkIfExists: true)
 				    ]
 				]
-				input[1] = GUNZIP.out.gunzip
-
+				input[1] = [
+				    [ id:'test', single_end:false ],
+				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists: true)
+				]
                 """
             }
         }
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 44c4d15b9ac4..21bf7cf6b71d 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -311,9 +311,3 @@ varlociraptor/callvariants:
 varlociraptor/preprocess:
   - modules/nf-core/varlociraptor/preprocess/**
   - tests/modules/nf-core/varlociraptor/preprocess/**
-vrhyme/extractunbinned:
-  - modules/nf-core/vrhyme/extractunbinned/**
-  - tests/modules/nf-core/vrhyme/extractunbinned/**
-vrhyme/linkbins:
-  - modules/nf-core/vrhyme/linkbins/**
-  - tests/modules/nf-core/vrhyme/linkbins/**
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/main.nf b/tests/modules/nf-core/vrhyme/extractunbinned/main.nf
deleted file mode 100644
index c30ee1b88213..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/main.nf
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP                    } from '../../../../../modules/nf-core/gunzip/main.nf'
-include { VRHYME_VRHYME             } from '../../../../../modules/nf-core/vrhyme/vrhyme/main.nf'
-include { VRHYME_EXTRACTUNBINNED    } from '../../../../../modules/nf-core/vrhyme/extractunbinned/main.nf'
-
-workflow test_vrhyme_extractunbinned {
-
-    reads = [
-        [ id:'test', single_end:false ], // meta map
-        [
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( fasta )
-
-    VRHYME_VRHYME ( reads , GUNZIP.out.gunzip )
-
-    VRHYME_EXTRACTUNBINNED ( VRHYME_VRHYME.out.membership , GUNZIP.out.gunzip )
-}
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config b/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/vrhyme/extractunbinned/test.yml b/tests/modules/nf-core/vrhyme/extractunbinned/test.yml
deleted file mode 100644
index 1c7dd18effae..000000000000
--- a/tests/modules/nf-core/vrhyme/extractunbinned/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: vrhyme extractunbinned test_vrhyme_extractunbinned
-  command: nextflow run ./tests/modules/nf-core/vrhyme/extractunbinned -entry test_vrhyme_extractunbinned -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config
-  tags:
-    - vrhyme
-    - vrhyme/extractunbinned
-  files:
-    - path: output/vrhyme/test_unbinned_sequences.fasta
-      md5sum: 816e986c8ad8f277eb4a4891a12d7aff
-    - path: output/vrhyme/versions.yml
-
-- name: vrhyme extractunbinned test_vrhyme_extractunbinned_stub
-  command: nextflow run ./tests/modules/nf-core/vrhyme/extractunbinned -entry test_vrhyme_extractunbinned -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/extractunbinned/nextflow.config -stub-run
-  tags:
-    - vrhyme
-    - vrhyme/extractunbinned
-  files:
-    - path: output/vrhyme/test_unbinned_sequences.fasta
-    - path: output/vrhyme/versions.yml
diff --git a/tests/modules/nf-core/vrhyme/linkbins/main.nf b/tests/modules/nf-core/vrhyme/linkbins/main.nf
deleted file mode 100644
index c03ac4d6ebc0..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/main.nf
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { GUNZIP            } from '../../../../../modules/nf-core/gunzip/main.nf'
-include { VRHYME_VRHYME     } from '../../../../../modules/nf-core/vrhyme/vrhyme/main.nf'
-include { VRHYME_LINKBINS   } from '../../../../../modules/nf-core/vrhyme/linkbins/main.nf'
-
-workflow test_vrhyme_linkbins {
-
-    reads = [
-        [ id:'test', single_end:false ], // meta map
-        [
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true)
-        ]
-    ]
-
-    fasta = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
-    ]
-
-    GUNZIP ( fasta )
-    VRHYME_VRHYME ( reads , GUNZIP.out.gunzip )
-    VRHYME_LINKBINS ( VRHYME_VRHYME.out.bins )
-}
diff --git a/tests/modules/nf-core/vrhyme/linkbins/nextflow.config b/tests/modules/nf-core/vrhyme/linkbins/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/vrhyme/linkbins/test.yml b/tests/modules/nf-core/vrhyme/linkbins/test.yml
deleted file mode 100644
index f4b3bbb698c1..000000000000
--- a/tests/modules/nf-core/vrhyme/linkbins/test.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-- name: vrhyme linkbins test_vrhyme_linkbins
-  command: nextflow run ./tests/modules/nf-core/vrhyme/linkbins -entry test_vrhyme_linkbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/linkbins/nextflow.config
-  tags:
-    - vrhyme/linkbins
-    - vrhyme
-  files:
-    - path: output/vrhyme/test_linked_bins.fasta
-      md5sum: 92cee5d85211d1e657f67ba75d3b2b30
-    - path: output/vrhyme/versions.yml
-
-- name: vrhyme linkbins test_vrhyme_linkbins_stub
-  command: nextflow run ./tests/modules/nf-core/vrhyme/linkbins -entry test_vrhyme_linkbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vrhyme/linkbins/nextflow.config -stub-run
-  tags:
-    - vrhyme/linkbins
-    - vrhyme
-  files:
-    - path: output/vrhyme/test_linked_bins.fasta
-    - path: output/vrhyme/versions.yml