diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index 3e95dd718a7..9c24eb0ab3c 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -1,8 +1,10 @@
 name: samtools_faidx
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
-  - bioconda::samtools=1.19.2
   - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.19.2
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index e189af28fd0..f3c25de20f4 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -39,6 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - fa:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa}"
   - fai:
       type: file
       description: FASTA index file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test
new file mode 100644
index 00000000000..136b2126797
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test
@@ -0,0 +1,123 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_FAIDX"
+    script "../main.nf"
+    process "SAMTOOLS_FAIDX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/faidx"
+
+    test("test_samtools_faidx") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_bgzip") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_fasta") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_stub_fasta") {
+
+        config "./nextflow2.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+    test("test_samtools_faidx_stub_fai") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+                input[1] = [[],[]]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        } 
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
new file mode 100644
index 00000000000..3e651ef680d
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -0,0 +1,249 @@
+{
+    "test_samtools_faidx": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:22:39.412601"
+    },
+    "test_samtools_faidx_bgzip": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:23:22.427966"
+    },
+    "test_samtools_faidx_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:24:04.107537"
+    },
+    "test_samtools_faidx_stub_fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "fai": [
+                    
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:24:45.868463"
+    },
+    "test_samtools_faidx_stub_fai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ],
+                "fa": [
+                    
+                ],
+                "fai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5"
+                    ]
+                ],
+                "gzi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T16:25:27.550554"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
new file mode 100644
index 00000000000..f76a3ba09b1
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = 'MT192765.1 -o extract.fa'
+    }
+
+}
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config
new file mode 100644
index 00000000000..33ebbd5df7f
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config
@@ -0,0 +1,6 @@
+process {
+
+    withName: SAMTOOLS_FAIDX {
+        ext.args = '-o extract.fa'
+    }
+}
diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml
new file mode 100644
index 00000000000..e4a839481d2
--- /dev/null
+++ b/modules/nf-core/samtools/faidx/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/faidx:
+  - modules/nf-core/samtools/faidx/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 379cc2b4057..6d006c915e1 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1844,9 +1844,6 @@ samtools/depth:
 samtools/dict:
   - modules/nf-core/samtools/dict/**
   - tests/modules/nf-core/samtools/dict/**
-samtools/faidx:
-  - modules/nf-core/samtools/faidx/**
-  - tests/modules/nf-core/samtools/faidx/**
 samtools/fasta:
   - modules/nf-core/samtools/fasta/**
   - tests/modules/nf-core/samtools/fasta/**
diff --git a/tests/modules/nf-core/samtools/faidx/main.nf b/tests/modules/nf-core/samtools/faidx/main.nf
deleted file mode 100644
index 8fa3bc6fa85..00000000000
--- a/tests/modules/nf-core/samtools/faidx/main.nf
+++ /dev/null
@@ -1,49 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SAMTOOLS_FAIDX } from '../../../../../modules/nf-core/samtools/faidx/main.nf'
-
-workflow test_samtools_faidx {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input, [[],[]] )
-}
-
-workflow test_samtools_faidx_bgzip {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input, [[],[]] )
-}
-
-workflow test_samtools_faidx_fasta {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    fai   = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input, fai )
-}
-
-workflow test_samtools_faidx_stub_fasta {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    fai   = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input, fai )
-}
-
-workflow test_samtools_faidx_stub_fai {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-
-    SAMTOOLS_FAIDX ( input, [[],[]] )
-}
diff --git a/tests/modules/nf-core/samtools/faidx/nextflow.config b/tests/modules/nf-core/samtools/faidx/nextflow.config
deleted file mode 100644
index cb1472e052e..00000000000
--- a/tests/modules/nf-core/samtools/faidx/nextflow.config
+++ /dev/null
@@ -1,11 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: 'test_samtools_faidx_fasta:SAMTOOLS_FAIDX' {
-        ext.args = 'MT192765.1 -o extract.fa'
-    }
-    withName: 'test_samtools_faidx_stub_fasta:SAMTOOLS_FAIDX' {
-        ext.args = '-o extract.fa'
-    }
-}
diff --git a/tests/modules/nf-core/samtools/faidx/test.yml b/tests/modules/nf-core/samtools/faidx/test.yml
deleted file mode 100644
index cc161244cc8..00000000000
--- a/tests/modules/nf-core/samtools/faidx/test.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-- name: samtools faidx test_samtools_faidx
-  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/faidx/nextflow.config
-  tags:
-    - samtools/faidx
-    - samtools
-  files:
-    - path: output/samtools/genome.fasta.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/samtools/versions.yml
-
-- name: samtools faidx test_samtools_faidx_bgzip
-  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/faidx/nextflow.config
-  tags:
-    - samtools/faidx
-    - samtools
-  files:
-    - path: output/samtools/genome.fasta.gz.fai
-      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
-    - path: output/samtools/genome.fasta.gz.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/samtools/versions.yml
-
-- name: samtools faidx test_samtools_faidx_fasta
-  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/faidx/nextflow.config
-  tags:
-    - samtools/faidx
-    - samtools
-  files:
-    - path: output/samtools/extract.fa
-    - path: output/samtools/versions.yml
-
-- name: samtools faidx test_samtools_faidx_stub_fasta
-  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_stub_fasta -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/faidx/nextflow.config -stub
-  tags:
-    - samtools/faidx
-    - samtools
-  files:
-    - path: output/samtools/extract.fa
-    - path: output/samtools/versions.yml
-
-- name: samtools faidx test_samtools_faidx_stub_fai
-  command: nextflow run ./tests/modules/nf-core/samtools/faidx -entry test_samtools_faidx_stub_fai -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/faidx/nextflow.config -stub
-  tags:
-    - samtools/faidx
-    - samtools
-  files:
-    - path: output/samtools/genome.fasta.fai
-    - path: output/samtools/versions.yml