diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3aa6b0eb..41b938d4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#674](https://github.com/nf-core/mag/pull/674) - Add porechop and filtlong logs to multiqc (added by @muabnezor)
 - [#674](https://github.com/nf-core/mag/pull/674) - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor)
 - [#690](https://github.com/nf-core/mag/pull/690) - MaxBin2 now using the abundance information from different samples rather than an average (reported by @uel3 and fixed by @d4straub)
+- [#698](https://github.com/nf-core/mag/pull/698) - Updated prodigal module to not pick up input symlinks for compression causing pigz errors (reported by @zackhenny, fix by @jfy133 )
 
 ### `Dependencies`
 
diff --git a/modules.json b/modules.json
index 21267891..c59a06f8 100644
--- a/modules.json
+++ b/modules.json
@@ -219,7 +219,7 @@
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml
new file mode 100644
index 00000000..7609bf3b
--- /dev/null
+++ b/modules/nf-core/prodigal/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::prodigal=2.6.3
+  - conda-forge::pigz=2.6
diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf
index 8cf87a6d..49ced167 100644
--- a/modules/nf-core/prodigal/main.nf
+++ b/modules/nf-core/prodigal/main.nf
@@ -2,7 +2,7 @@ process PRODIGAL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
         'biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
@@ -33,7 +33,10 @@ process PRODIGAL {
         -a "${prefix}.faa" \\
         -s "${prefix}_all.txt"
 
-    pigz -nm ${prefix}*
+    pigz -nm ${prefix}.fna
+    pigz -nm ${prefix}.${output_format}
+    pigz -nm ${prefix}.faa
+    pigz -nm ${prefix}_all.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -41,4 +44,21 @@ process PRODIGAL {
         pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args   ?: ''
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fna.gz
+    touch ${prefix}.${output_format}.gz
+    touch ${prefix}.faa.gz
+    touch ${prefix}_all.txt.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
+        pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/prodigal/meta.yml b/modules/nf-core/prodigal/meta.yml
index 30747a90..7d3d459e 100644
--- a/modules/nf-core/prodigal/meta.yml
+++ b/modules/nf-core/prodigal/meta.yml
@@ -1,57 +1,79 @@
 name: prodigal
-description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
+description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
+  microbial (bacterial and archaeal) gene finding program
 keywords:
   - prokaryotes
   - gene finding
   - microbial
 tools:
   - prodigal:
-      description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
+      description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
+        is a microbial (bacterial and archaeal) gene finding program
       homepage: https://github.com/hyattpd/Prodigal
       documentation: https://github.com/hyattpd/prodigal/wiki
       tool_dev_url: https://github.com/hyattpd/Prodigal
       doi: "10.1186/1471-2105-11-119"
       licence: ["GPL v3"]
-
+      identifier: biotools:prodigal
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - genome:
-      type: file
-      description: fasta/fasta.gz file
-  - output_format:
-      type: string
-      description: Output format ("gbk"/"gff"/"sqn"/"sco")
-
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - genome:
+        type: file
+        description: fasta/fasta.gz file
+  - - output_format:
+        type: string
+        description: Output format ("gbk"/"gff"/"sqn"/"sco")
 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"
+  - gene_annotations:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.${output_format}.gz:
+          type: file
+          description: gene annotations in output_format given as input
+          pattern: "*.{output_format}"
   - nucleotide_fasta:
-      type: file
-      description: nucleotide sequences file
-      pattern: "*.{fna}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.fna.gz:
+          type: file
+          description: nucleotide sequences file
+          pattern: "*.{fna}"
   - amino_acid_fasta:
-      type: file
-      description: protein translations file
-      pattern: "*.{faa}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}.faa.gz:
+          type: file
+          description: protein translations file
+          pattern: "*.{faa}"
   - all_gene_annotations:
-      type: file
-      description: complete starts file
-      pattern: "*.{_all.txt}"
-  - gene_annotations:
-      type: file
-      description: gene annotations in output_format given as input
-      pattern: "*.{output_format}"
-
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}_all.txt.gz:
+          type: file
+          description: complete starts file
+          pattern: "*.{_all.txt}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@grst"
+maintainers:
+  - "@grst"
diff --git a/modules/nf-core/prodigal/tests/main.nf.test b/modules/nf-core/prodigal/tests/main.nf.test
new file mode 100644
index 00000000..446bd0d1
--- /dev/null
+++ b/modules/nf-core/prodigal/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process PRODIGAL"
+    script "../main.nf"
+    process "PRODIGAL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "prodigal"
+
+    test("prodigal - sarscov2 - gff") {
+        when {
+            process {
+                """
+                input[0] = [
+                            [id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                           ]
+                input[1] =  'gff'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("prodigal - sarscov2 - gbk") {
+        when {
+            process {
+                """
+                input[0] = [
+                            [id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                           ]
+                input[1] =  'gbk'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("prodigal - sarscov2 - gff - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                           ]
+                input[1] =  'gff'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.out).match() }
+            )
+        }
+    }
+
+    test("prodigal - sarscov2 - gbk - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [id:'test', single_end:false ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                           ]
+                input[1] =  'gbk'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.out).match() }
+            )
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/prodigal/tests/main.nf.test.snap b/modules/nf-core/prodigal/tests/main.nf.test.snap
new file mode 100644
index 00000000..f29802b4
--- /dev/null
+++ b/modules/nf-core/prodigal/tests/main.nf.test.snap
@@ -0,0 +1,196 @@
+{
+    "prodigal - sarscov2 - gbk - stub": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T13:58:09.852618454"
+    },
+    "prodigal - sarscov2 - gff": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gff.gz:md5,612c2724c2891c63350f171f74165757"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,9541e53a6927e9856036bb97bfb30307"
+                ],
+                "all_gene_annotations": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9"
+                    ]
+                ],
+                "amino_acid_fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
+                    ]
+                ],
+                "gene_annotations": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gff.gz:md5,612c2724c2891c63350f171f74165757"
+                    ]
+                ],
+                "nucleotide_fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9541e53a6927e9856036bb97bfb30307"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T13:57:49.57989696"
+    },
+    "prodigal - sarscov2 - gff - stub": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T13:58:03.210222528"
+    },
+    "prodigal - sarscov2 - gbk": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gbk.gz:md5,188b3a0e3f78740ded7f3ec4d876cb4b"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9"
+                    ]
+                ],
+                "4": [
+                    "versions.yml:md5,9541e53a6927e9856036bb97bfb30307"
+                ],
+                "all_gene_annotations": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_all.txt.gz:md5,e6d6c50f0c39e5169f84ae3c90837fa9"
+                    ]
+                ],
+                "amino_acid_fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.faa.gz:md5,7168b854103f3586ccfdb71a44c389f7"
+                    ]
+                ],
+                "gene_annotations": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.gbk.gz:md5,188b3a0e3f78740ded7f3ec4d876cb4b"
+                    ]
+                ],
+                "nucleotide_fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fna.gz:md5,1bc8a05bcb72a3c324f5e4ffaa716d3b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9541e53a6927e9856036bb97bfb30307"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T13:57:56.606374214"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/prodigal/tests/tags.yml b/modules/nf-core/prodigal/tests/tags.yml
new file mode 100644
index 00000000..fc0cb020
--- /dev/null
+++ b/modules/nf-core/prodigal/tests/tags.yml
@@ -0,0 +1,2 @@
+prodigal:
+  - "modules/nf-core/prodigal/**"