diff --git a/.cache.tar.xz b/.cache.tar.xz
index 31238a5484..0bf795ecc9 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index 289f349ff7..d45213eb67 100644
--- a/public/components.json
+++ b/public/components.json
@@ -7768,6 +7768,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -25578,6 +25582,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -72538,7 +72550,7 @@
             {
               "input": {
                 "type": "file",
-                "description": "The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file",
+                "description": "The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file. If the files have a `.gz` extension, they will be unzipped using `zcat`.",
                 "pattern": "*"
               }
             }
@@ -107638,6 +107650,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -199204,6 +199220,10 @@
           "name": "demo",
           "version": "1.0.1"
         },
+        {
+          "name": "methylarray",
+          "version": "dev"
+        },
         {
           "name": "phaseimpute",
           "version": "dev"
@@ -199383,10 +199403,6 @@
           "name": "metapep",
           "version": "dev"
         },
-        {
-          "name": "methylarray",
-          "version": "dev"
-        },
         {
           "name": "mhcquant",
           "version": "2.6.0"
diff --git a/public/pipelines.json b/public/pipelines.json
index 376b6611e7..d7c44dcd12 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -20756,10 +20756,10 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/methylarray",
             "created_at": "2024-08-29T12:05:47Z",
-            "updated_at": "2024-10-17T15:52:05Z",
-            "pushed_at": "2024-10-17T15:52:01Z",
+            "updated_at": "2024-10-20T13:45:04Z",
+            "pushed_at": "2024-10-20T13:45:01Z",
             "homepage": null,
-            "size": 31246,
+            "size": 31253,
             "stargazers_count": 2,
             "watchers_count": 2,
             "language": "Nextflow",
@@ -20772,14 +20772,14 @@
             "forks_count": 0,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 1,
+            "open_issues_count": 0,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 0,
-            "open_issues": 1,
+            "open_issues": 0,
             "watchers": 2,
             "default_branch": "dev",
             "temp_clone_token": "",
@@ -20843,12 +20843,12 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": -1,
             "has_required_topics": false,
-            "open_pr_count": 1,
+            "open_pr_count": 0,
             "repository_url": "https://github.com/nf-core/methylarray",
             "contributors": [
                 {
                     "name": "ajandria",
-                    "count": 14,
+                    "count": 19,
                     "avatar_url": "https://avatars.githubusercontent.com/u/12818785?v=4"
                 },
                 {
@@ -20858,24 +20858,24 @@
                 }
             ],
             "released_after_tools": false,
-            "head_sha": "5ffc328906fe22801594e9c3af71d8a4b972179e",
+            "head_sha": "35fc82aa284a1abe4d0248074d438aca43d44457",
             "last_release_is_head": false,
-            "last_release_vs_default_compare_url": "https://github.com/nf-core/methylarray/compare/5ffc328906fe22801594e9c3af71d8a4b972179e...undefined",
-            "commits_to_dev": 15,
+            "last_release_vs_default_compare_url": "https://github.com/nf-core/methylarray/compare/35fc82aa284a1abe4d0248074d438aca43d44457...undefined",
+            "commits_to_dev": 23,
             "is_DSL2": true,
             "has_nf_test": false,
             "has_nf_test_dev": false,
             "master_nextflow_config_plugins": [
-                "nf-validation@1.1.3"
+                "nf-schema@2.1.1"
             ],
             "dev_nextflow_config_plugins": [
-                "nf-validation@1.1.3"
+                "nf-schema@2.1.1"
             ],
             "releases": [
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-10-17T15:51:48Z",
-                    "tag_sha": "5ffc328906fe22801594e9c3af71d8a4b972179e",
+                    "published_at": "2024-10-20T13:41:57Z",
+                    "tag_sha": "35fc82aa284a1abe4d0248074d438aca43d44457",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -20889,7 +20889,7 @@
                         "subworkflows": [
                             "utils_nextflow_pipeline",
                             "utils_nfcore_pipeline",
-                            "utils_nfvalidation_plugin"
+                            "utils_nfschema_plugin"
                         ]
                     }
                 }
@@ -20921,7 +20921,7 @@
             "forks_count": 143,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 46,
+            "open_issues_count": 47,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -20937,7 +20937,7 @@
             ],
             "visibility": "public",
             "forks": 143,
-            "open_issues": 46,
+            "open_issues": 47,
             "watchers": 138,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -21018,7 +21018,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 4,
+            "open_pr_count": 5,
             "repository_url": "https://github.com/nf-core/methylseq",
             "contributors": [
                 {
@@ -23510,9 +23510,9 @@
             "url": "https://api.github.com/repos/nf-core/nascent",
             "created_at": "2018-11-15T15:46:09Z",
             "updated_at": "2024-09-06T05:39:17Z",
-            "pushed_at": "2024-10-20T00:25:01Z",
+            "pushed_at": "2024-10-20T02:51:18Z",
             "homepage": "https://nf-co.re/nascent",
-            "size": 8724,
+            "size": 8723,
             "stargazers_count": 18,
             "watchers_count": 18,
             "language": "Nextflow",
@@ -34644,7 +34644,7 @@
             "forks_count": 404,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 282,
+            "open_issues_count": 283,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -34663,7 +34663,7 @@
             ],
             "visibility": "public",
             "forks": 404,
-            "open_issues": 282,
+            "open_issues": 283,
             "watchers": 400,
             "default_branch": "master",
             "temp_clone_token": "",