diff --git a/modules/nf-core/pilon/main.nf b/modules/nf-core/pilon/main.nf
index ff610b0ad14..8e476db8e8c 100644
--- a/modules/nf-core/pilon/main.nf
+++ b/modules/nf-core/pilon/main.nf
@@ -9,7 +9,7 @@ process PILON {
 
     input:
     tuple val(meta), path(fasta)
-    tuple val(meta_bam), path(bam), path(bai)
+    tuple val(meta2), path(bam), path(bai)
     val pilon_mode
 
     output:
@@ -24,8 +24,8 @@ process PILON {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
     def valid_mode = ["frags", "jumps", "unpaired", "bam"]
     if ( !valid_mode.contains(pilon_mode) )  { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
     """
@@ -39,5 +39,24 @@ process PILON {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
     """
+
+    stub:
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    def valid_mode = ["frags", "jumps", "unpaired", "bam"]
+    if ( !valid_mode.contains(pilon_mode) )  { error "Unrecognised mode to run Pilon. Options: ${valid_mode.join(', ')}" }
+    """
+    touch ${prefix}.fasta
+    touch ${prefix}.vcf
+    touch ${prefix}.change
+    touch ${prefix}.bed
+    touch ${prefix}.wig
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pilon: \$(echo \$(pilon --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/pilon/meta.yml b/modules/nf-core/pilon/meta.yml
index 6a395a204e2..7a11c4dde1a 100644
--- a/modules/nf-core/pilon/meta.yml
+++ b/modules/nf-core/pilon/meta.yml
@@ -11,17 +11,22 @@ tools:
       documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage"
       tool_dev_url: "https://github.com/broadinstitute/pilon"
       doi: "10.1371/journal.pone.0112963"
-      licence: "['GPL v2']"
+      licence: ["GPL-2.0-or-later"]
 input:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
+        Groovy Map containing sample information for the fasta
         e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: FASTA of the input genome
       pattern: "*.{fasta}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information for the bam file
+        e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
       description: BAM file of reads aligned to the input genome
diff --git a/modules/nf-core/pilon/tests/main.nf.test b/modules/nf-core/pilon/tests/main.nf.test
new file mode 100644
index 00000000000..2d09e8b85a6
--- /dev/null
+++ b/modules/nf-core/pilon/tests/main.nf.test
@@ -0,0 +1,116 @@
+nextflow_process {
+
+    name "Test Process PILON"
+    script "../main.nf"
+    process "PILON"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pilon"
+
+
+    test("homo sapiens bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "bam"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens bam - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "bam"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens frags") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "frags"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens frags - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true)
+                            ]
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                               file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                               file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true),
+                            ]
+                input[2] = "frags"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/pilon/tests/main.nf.test.snap b/modules/nf-core/pilon/tests/main.nf.test.snap
new file mode 100644
index 00000000000..91208228b89
--- /dev/null
+++ b/modules/nf-core/pilon/tests/main.nf.test.snap
@@ -0,0 +1,334 @@
+{
+    "homo sapiens bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.change:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ],
+                "change_record": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.change:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "improved_assembly": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tracks_bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tracks_wig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-27T13:18:02.740029689"
+    },
+    "homo sapiens bam": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,2e881994820a5a641da9ea594ab4958f"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ],
+                "change_record": [
+                    
+                ],
+                "improved_assembly": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,2e881994820a5a641da9ea594ab4958f"
+                    ]
+                ],
+                "tracks_bed": [
+                    
+                ],
+                "tracks_wig": [
+                    
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-14T11:20:04.988498289"
+    },
+    "homo sapiens frags": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,2e881994820a5a641da9ea594ab4958f"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ],
+                "change_record": [
+                    
+                ],
+                "improved_assembly": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,2e881994820a5a641da9ea594ab4958f"
+                    ]
+                ],
+                "tracks_bed": [
+                    
+                ],
+                "tracks_wig": [
+                    
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-14T11:29:53.995788701"
+    },
+    "homo sapiens frags - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.change:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ],
+                "change_record": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.change:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "improved_assembly": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tracks_bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tracks_wig": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.wig:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,73f60b48e5c3838296b66520b61a551a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-27T13:18:31.732478412"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pilon/tests/tags.yml b/modules/nf-core/pilon/tests/tags.yml
new file mode 100644
index 00000000000..0d94efba1d7
--- /dev/null
+++ b/modules/nf-core/pilon/tests/tags.yml
@@ -0,0 +1,2 @@
+pilon:
+  - "modules/nf-core/pilon/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a0f69406b34..8b987cb0801 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1235,9 +1235,6 @@ picard/sortsam:
 picard/sortvcf:
   - modules/nf-core/picard/sortvcf/**
   - tests/modules/nf-core/picard/sortvcf/**
-pilon:
-  - modules/nf-core/pilon/**
-  - tests/modules/nf-core/pilon/**
 pindel/pindel:
   - modules/nf-core/pindel/pindel/**
   - tests/modules/nf-core/pindel/pindel/**
diff --git a/tests/modules/nf-core/pilon/main.nf b/tests/modules/nf-core/pilon/main.nf
deleted file mode 100644
index 7adfb149a80..00000000000
--- a/tests/modules/nf-core/pilon/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PILON } from '../../../../modules/nf-core/pilon/main.nf'
-
-workflow test_pilon {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-
-    bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-                                ])
-
-    PILON ( input, bam_tuple_ch, "bam" )
-}
diff --git a/tests/modules/nf-core/pilon/nextflow.config b/tests/modules/nf-core/pilon/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/pilon/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/pilon/test.yml b/tests/modules/nf-core/pilon/test.yml
deleted file mode 100644
index 2e36a64d5fe..00000000000
--- a/tests/modules/nf-core/pilon/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: pilon test_pilon
-  command: nextflow run ./tests/modules/nf-core/pilon -entry test_pilon -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pilon/nextflow.config
-  tags:
-    - pilon
-  files:
-    - path: output/pilon/test.fasta
-      md5sum: 2e881994820a5a641da9ea594ab4958f
-    - path: output/pilon/versions.yml