[automated] Update json files

Author: nf-core-bot

public/components.json

@@ -152610,10 +152610,10 @@
               }
             },
             {
-              "fasta": {
+              "ref": {
                 "type": "file",
                 "description": "A reference file to calculate dropout metrics measuring reduced representation of reads.\nOptional input.\n",
-                "pattern": "*.{fa,fasta,fna}",
+                "pattern": "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}",
                 "ontologies": []
               }
             }
@@ -152626,9 +152626,9 @@
               }
             },
             {
-              "fai": {
+              "ref_fai": {
                 "type": "file",
-                "description": "Index of FASTA file. Only needed when fasta is supplied.",
+                "description": "Index of reference file. Only needed when reference is supplied.",
                 "pattern": "*.fai",
                 "ontologies": []
               }
@@ -152642,13 +152642,29 @@
               }
             },
             {
-              "dict": {
+              "ref_dict": {
                 "type": "file",
                 "description": "Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.",
                 "pattern": "*.dict",
                 "ontologies": []
               }
             }
+          ],
+          [
+            {
+              "meta5": {
+                "type": "map",
+                "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+              }
+            },
+            {
+              "ref_gzi": {
+                "type": "file",
+                "description": "Index of reference file. Only needed when gzipped reference is supplied.",
+                "pattern": "*.gzi",
+                "ontologies": []
+              }
+            }
           ]
         ],
         "output": {

public/pipelines.json

@@ -5239,7 +5239,7 @@
             "has_wiki": false,
             "has_pages": false,
             "has_discussions": false,
-            "forks_count": 32,
+            "forks_count": 33,
             "archived": false,
             "disabled": false,
             "open_issues_count": 13,
@@ -5258,7 +5258,7 @@
                 "rna-seq"
             ],
             "visibility": "public",
-            "forks": 32,
+            "forks": 33,
             "open_issues": 13,
             "watchers": 57,
             "default_branch": "dev",
@@ -5295,7 +5295,7 @@
                     "status": "enabled"
                 }
             },
-            "network_count": 32,
+            "network_count": 33,
             "subscribers_count": 128,
             "team_contributors_permission_push": true,
             "team_contributors_permission_admin": false,
@@ -16453,7 +16453,7 @@
             "has_wiki": false,
             "has_pages": false,
             "has_discussions": false,
-            "forks_count": 24,
+            "forks_count": 25,
             "archived": false,
             "disabled": false,
             "open_issues_count": 14,
@@ -16464,7 +16464,7 @@
                 "gwas"
             ],
             "visibility": "public",
-            "forks": 24,
+            "forks": 25,
             "open_issues": 14,
             "watchers": 26,
             "default_branch": "dev",
@@ -16501,7 +16501,7 @@
                     "status": "enabled"
                 }
             },
-            "network_count": 24,
+            "network_count": 25,
             "subscribers_count": 177,
             "team_contributors_permission_push": true,
             "team_contributors_permission_admin": false,
@@ -29402,14 +29402,14 @@
             "forks_count": 7,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 64,
+            "open_issues_count": 65,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 7,
-            "open_issues": 64,
+            "open_issues": 65,
             "watchers": 43,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -37196,12 +37196,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/rnaseq",
             "created_at": "2018-03-29T13:10:58Z",
-            "updated_at": "2025-09-04T04:29:59Z",
+            "updated_at": "2025-09-07T03:19:37Z",
             "pushed_at": "2025-09-05T16:13:30Z",
             "homepage": "https://nf-co.re/rnaseq",
             "size": 76052,
-            "stargazers_count": 1094,
-            "watchers_count": 1094,
+            "stargazers_count": 1095,
+            "watchers_count": 1095,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -37223,7 +37223,7 @@
             "visibility": "public",
             "forks": 795,
             "open_issues": 78,
-            "watchers": 1094,
+            "watchers": 1095,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,