diff --git a/modules/nf-core/pyrodigal/environment.yml b/modules/nf-core/pyrodigal/environment.yml
index b0bbc5158862..26be9f32df19 100644
--- a/modules/nf-core/pyrodigal/environment.yml
+++ b/modules/nf-core/pyrodigal/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::pyrodigal=3.3.0
+  - bioconda::pyrodigal=3.6.3
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/pyrodigal/main.nf b/modules/nf-core/pyrodigal/main.nf
index 7cb97594b29b..9cbe8fcc9419 100644
--- a/modules/nf-core/pyrodigal/main.nf
+++ b/modules/nf-core/pyrodigal/main.nf
@@ -1,11 +1,11 @@
 process PYRODIGAL {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0':
-        'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:da1134ad604a59a6f439bdcc3f6df690eba47e9a-0':
+        'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:da1134ad604a59a6f439bdcc3f6df690eba47e9a-0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -28,6 +28,7 @@ process PYRODIGAL {
     pigz -cdf ${fasta} > pigz_fasta.fna
 
     pyrodigal \\
+        -j ${task.cpus} \\
         $args \\
         -i pigz_fasta.fna \\
         -f $output_format \\
diff --git a/modules/nf-core/pyrodigal/tests/main.nf.test.snap b/modules/nf-core/pyrodigal/tests/main.nf.test.snap
index 827fdaaa3572..3d56b9f1f881 100644
--- a/modules/nf-core/pyrodigal/tests/main.nf.test.snap
+++ b/modules/nf-core/pyrodigal/tests/main.nf.test.snap
@@ -5,21 +5,21 @@
                 "test.fna.gz",
                 "test.faa.gz",
                 "test.score.gz",
-                "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+                "versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-03-18T15:42:12.012112014"
+        "timestamp": "2024-12-02T15:17:12.218638993"
     },
     "pyrodigal - sarscov2 - gbk": {
         "content": [
             [
                 "     CDS             310..13476",
                 "                     /codon_start=1",
-                "                     /inference=\"ab initio prediction:pyrodigal:3.3.0\"",
+                "                     /inference=\"ab initio prediction:pyrodigal:3.6.3\"",
                 "                     /locus_tag=\"MT192765.1_1\"",
                 "                     /transl_table=11",
                 "                     /translation=\"MPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLP",
@@ -51,18 +51,18 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
+                    "test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
                 ]
             ],
             [
-                "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+                "versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-30T06:09:40.289778252"
+        "timestamp": "2024-12-02T15:17:01.228814939"
     },
     "pyrodigal - sarscov2 - gff": {
         "content": [
@@ -73,7 +73,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27"
+                        "test.gff.gz:md5,898c1e24e71fa108981597b8bb32110f"
                     ]
                 ],
                 "1": [
@@ -100,11 +100,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
+                        "test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+                    "versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
                 ],
                 "annotations": [
                     [
@@ -112,7 +112,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27"
+                        "test.gff.gz:md5,898c1e24e71fa108981597b8bb32110f"
                     ]
                 ],
                 "faa": [
@@ -139,19 +139,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
+                        "test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+                    "versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-03-18T15:41:55.822235843"
+        "timestamp": "2024-12-02T15:16:49.907998584"
     },
     "pyrodigal - sarscov2 - gbk - stub": {
         "content": [
@@ -159,13 +159,13 @@
                 "test.fna.gz",
                 "test.faa.gz",
                 "test.score.gz",
-                "versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
+                "versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-03-18T15:42:19.81157751"
+        "timestamp": "2024-12-02T15:17:22.681680508"
     }
 }
\ No newline at end of file