diff --git a/.cache.tar.xz b/.cache.tar.xz
index d78ff470f7..1ee9d2f3ac 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index 0e596720a5..04dbbe5e46 100644
--- a/public/components.json
+++ b/public/components.json
@@ -7604,6 +7604,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -13441,13 +13445,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.{vcf.gz}"
                 }
               },
               {
-                "*.gz": {
-                  "type": "file",
-                  "description": "VCF concatenated output file",
+                "${prefix}.vcf.gz": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.{vcf.gz}"
                 }
               }
@@ -13458,13 +13463,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.tbi"
                 }
               },
               {
-                "*.tbi": {
-                  "type": "file",
-                  "description": "Alternative VCF file index",
+                "${prefix}.vcf.gz.tbi": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.tbi"
                 }
               }
@@ -13475,13 +13481,14 @@
               {
                 "meta": {
                   "type": "map",
-                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
+                  "pattern": "*.csi"
                 }
               },
               {
-                "*.csi": {
-                  "type": "file",
-                  "description": "Default VCF file index",
+                "${prefix}.vcf.gz.csi": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n",
                   "pattern": "*.csi"
                 }
               }
@@ -24708,6 +24715,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -106133,6 +106148,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
diff --git a/public/pipelines.json b/public/pipelines.json
index 6fb504e78b..ddaa2ed81a 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -23,7 +23,7 @@
             "has_wiki": false,
             "has_pages": false,
             "has_discussions": false,
-            "forks_count": 33,
+            "forks_count": 34,
             "archived": false,
             "disabled": false,
             "open_issues_count": 22,
@@ -38,7 +38,7 @@
                 "repseq"
             ],
             "visibility": "public",
-            "forks": 33,
+            "forks": 34,
             "open_issues": 22,
             "watchers": 52,
             "default_branch": "master",
@@ -72,7 +72,7 @@
                     "status": "disabled"
                 }
             },
-            "network_count": 33,
+            "network_count": 34,
             "subscribers_count": 144,
             "team_contributors_permission_push": true,
             "team_contributors_permission_admin": false,
@@ -534,7 +534,7 @@
             "forks_count": 114,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 24,
+            "open_issues_count": 25,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -557,7 +557,7 @@
             ],
             "visibility": "public",
             "forks": 114,
-            "open_issues": 24,
+            "open_issues": 25,
             "watchers": 182,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -3703,23 +3703,13 @@
                 "url": "https://api.github.com/repos/nf-core/chipseq/branches/master/protection/required_status_checks",
                 "strict": false,
                 "contexts": [
-                    "nf-core",
-                    "Prettier",
-                    "EditorConfig"
+                    "nf-core"
                 ],
                 "contexts_url": "https://api.github.com/repos/nf-core/chipseq/branches/master/protection/required_status_checks/contexts",
                 "checks": [
                     {
                         "context": "nf-core",
                         "app_id": null
-                    },
-                    {
-                        "context": "Prettier",
-                        "app_id": 15368
-                    },
-                    {
-                        "context": "EditorConfig",
-                        "app_id": 15368
                     }
                 ]
             },
@@ -10630,12 +10620,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/eager",
             "created_at": "2018-06-03T15:52:24Z",
-            "updated_at": "2024-09-18T04:06:49Z",
+            "updated_at": "2024-09-26T14:50:40Z",
             "pushed_at": "2024-09-25T16:38:44Z",
             "homepage": "https://nf-co.re/eager",
             "size": 67285,
-            "stargazers_count": 142,
-            "watchers_count": 142,
+            "stargazers_count": 143,
+            "watchers_count": 143,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -10662,7 +10652,7 @@
             "visibility": "public",
             "forks": 80,
             "open_issues": 43,
-            "watchers": 142,
+            "watchers": 143,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -12078,12 +12068,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/fetchngs",
             "created_at": "2021-06-03T09:26:41Z",
-            "updated_at": "2024-09-25T03:57:18Z",
+            "updated_at": "2024-09-26T19:10:06Z",
             "pushed_at": "2024-09-24T20:27:23Z",
             "homepage": "https://nf-co.re/fetchngs",
             "size": 4026,
-            "stargazers_count": 147,
-            "watchers_count": 147,
+            "stargazers_count": 148,
+            "watchers_count": 148,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": true,
@@ -12110,7 +12100,7 @@
             "visibility": "public",
             "forks": 72,
             "open_issues": 29,
-            "watchers": 147,
+            "watchers": 148,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -15810,12 +15800,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/isoseq",
             "created_at": "2022-06-03T10:07:33Z",
-            "updated_at": "2024-09-05T16:17:53Z",
+            "updated_at": "2024-09-26T21:11:09Z",
             "pushed_at": "2024-09-05T16:19:40Z",
             "homepage": "https://nf-co.re/isoseq",
             "size": 5259,
-            "stargazers_count": 27,
-            "watchers_count": 27,
+            "stargazers_count": 28,
+            "watchers_count": 28,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": true,
@@ -15840,7 +15830,7 @@
             "visibility": "public",
             "forks": 13,
             "open_issues": 3,
-            "watchers": 27,
+            "watchers": 28,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -23105,9 +23095,9 @@
             "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": "2024-09-25T21:33:47Z",
+            "pushed_at": "2024-09-26T19:57:03Z",
             "homepage": "https://nf-co.re/nascent",
-            "size": 8571,
+            "size": 8560,
             "stargazers_count": 18,
             "watchers_count": 18,
             "language": "Nextflow",
@@ -23120,7 +23110,7 @@
             "forks_count": 10,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 40,
+            "open_issues_count": 42,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -23134,7 +23124,7 @@
             ],
             "visibility": "public",
             "forks": 10,
-            "open_issues": 40,
+            "open_issues": 42,
             "watchers": 18,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -23232,7 +23222,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 4,
+            "open_pr_count": 6,
             "repository_url": "https://github.com/nf-core/nascent",
             "contributors": [
                 {
@@ -24006,7 +23996,7 @@
             "url": "https://api.github.com/repos/nf-core/oncoanalyser",
             "created_at": "2022-12-22T05:01:49Z",
             "updated_at": "2024-09-15T18:34:09Z",
-            "pushed_at": "2024-09-26T07:15:33Z",
+            "pushed_at": "2024-09-26T15:23:35Z",
             "homepage": "https://nf-co.re/oncoanalyser",
             "size": 4909,
             "stargazers_count": 40,
@@ -39247,7 +39237,7 @@
             "forks_count": 124,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 19,
+            "open_issues_count": 20,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -39257,7 +39247,7 @@
             ],
             "visibility": "public",
             "forks": 124,
-            "open_issues": 19,
+            "open_issues": 20,
             "watchers": 72,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -39345,7 +39335,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 2,
+            "open_pr_count": 3,
             "repository_url": "https://github.com/nf-core/smrnaseq",
             "contributors": [
                 {