diff --git a/.cache.tar.xz b/.cache.tar.xz
index fbe4398fc6..5c46d86017 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index f90db8cd55..426ed8fc9c 100644
--- a/public/components.json
+++ b/public/components.json
@@ -8712,6 +8712,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -43969,7 +43973,7 @@
                 }
               },
               {
-                "R_sessionInfo.log": {
+                "*R_sessionInfo.log": {
                   "type": "file",
                   "description": "Log file containing R session information",
                   "pattern": "*.log"
@@ -83968,6 +83972,164 @@
         }
       ]
     },
+    {
+      "name": "gridss_generateponbedpe",
+      "path": "modules/nf-core/gridss/generateponbedpe/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "gridss_generateponbedpe",
+        "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.",
+        "keywords": [
+          "gridss",
+          "structural variants",
+          "bedpe",
+          "bed",
+          "vcf"
+        ],
+        "tools": [
+          {
+            "gridss": {
+              "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite",
+              "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation",
+              "tool_dev_url": "https://github.com/PapenfussLab/gridss",
+              "doi": "10.1186/s13059-021-02423-x",
+              "licence": [
+                "GPL v3"
+              ],
+              "identifier": "biotools:gridss"
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "vcf": {
+                "type": "file",
+                "description": "GRIDSS generated vcf file",
+                "pattern": "*.vcf"
+              }
+            },
+            {
+              "bedpe": {
+                "type": "file",
+                "description": "GRIDSS generated bedpe file",
+                "pattern": "*.bedpe"
+              }
+            },
+            {
+              "bed": {
+                "type": "file",
+                "description": "GRIDSS generated bed file",
+                "pattern": "*.bed"
+              }
+            }
+          ],
+          [
+            {
+              "meta2": {
+                "type": "map",
+                "description": "Groovy Map containing reference information\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "fasta": {
+                "type": "file",
+                "description": "The reference fasta",
+                "pattern": "*.{fa,fna,fasta}"
+              }
+            }
+          ],
+          [
+            {
+              "meta3": {
+                "type": "map",
+                "description": "Groovy Map containing reference fai information\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "fai": {
+                "type": "file",
+                "description": "The index of the reference fasta",
+                "pattern": "*.fai"
+              }
+            }
+          ],
+          [
+            {
+              "meta4": {
+                "type": "map",
+                "description": "Groovy Map containing bwa generated index information\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "bwa_index": {
+                "type": "directory",
+                "description": "OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step"
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "bedpe": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n"
+                }
+              },
+              {
+                "*.bedpe": {
+                  "type": "file",
+                  "description": "GRIDSS generated breakpoint pon bedpe file",
+                  "pattern": "*.bedpe"
+                }
+              }
+            ]
+          },
+          {
+            "bed": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n"
+                }
+              },
+              {
+                "*.bed": {
+                  "type": "file",
+                  "description": "GRIDSS generated breakpoint pon bed file",
+                  "pattern": "*.bed"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@kubranarci"
+        ],
+        "maintainers": [
+          "@famosab"
+        ]
+      }
+    },
     {
       "name": "gridss_gridss",
       "path": "modules/nf-core/gridss/gridss/meta.yml",
@@ -84360,6 +84522,119 @@
         ]
       }
     },
+    {
+      "name": "gridss_somaticfilter",
+      "path": "modules/nf-core/gridss/somaticfilter/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "gridss_somaticfilter",
+        "description": "GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.",
+        "keywords": [
+          "gridss",
+          "structural variants",
+          "somatic variants",
+          "vcf"
+        ],
+        "tools": [
+          {
+            "gridss": {
+              "description": "GRIDSS: the Genomic Rearrangement IDentification Software Suite",
+              "documentation": "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation",
+              "tool_dev_url": "https://github.com/PapenfussLab/gridss",
+              "doi": "10.1186/s13059-021-02423-x",
+              "licence": [
+                "GPL v3"
+              ],
+              "identifier": "biotools:gridss"
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "vcf": {
+                "type": "file",
+                "description": "Input VCF file, must be generated with GRIDSS",
+                "pattern": "*.{vcf,vcf.gz}"
+              }
+            }
+          ],
+          [
+            {
+              "meta2": {
+                "type": "map",
+                "description": "Groovy Map containing information for PONDIR\ne.g. [ id:'test']\n"
+              }
+            },
+            {
+              "pondir": {
+                "type": "directory",
+                "description": "Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON."
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "high_conf_sv": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n"
+                }
+              },
+              {
+                "*.high_confidence_somatic.vcf.bgz": {
+                  "type": "file",
+                  "description": "VCF file including high confidence somatic SVs",
+                  "pattern": "*.vcf.bgz"
+                }
+              }
+            ]
+          },
+          {
+            "all_sv": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. [ id:'test']\n"
+                }
+              },
+              {
+                "*.all_somatic.vcf.bgz": {
+                  "type": "file",
+                  "description": "VCF file including all somatic SVs",
+                  "pattern": "*.vcf.bgz"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@kubranarci"
+        ],
+        "maintainers": [
+          "@famosab"
+        ]
+      }
+    },
     {
       "name": "gsea_gsea",
       "path": "modules/nf-core/gsea/gsea/meta.yml",
@@ -99577,6 +99852,15 @@
                 "pattern": "*.{fa,faa,fasta}"
               }
             }
+          ],
+          [
+            {
+              "keep_intermediate": {
+                "type": "boolean",
+                "description": "Keep intermediate files",
+                "pattern": "true|false"
+              }
+            }
           ]
         ],
         "output": [
@@ -99597,6 +99881,40 @@
               }
             ]
           },
+          {
+            "bwt": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n"
+                }
+              },
+              {
+                "*.bwt": {
+                  "type": "file",
+                  "description": "Kaiju intermedite bwt-index file (not needed for classification)",
+                  "pattern": "*.{bwt}"
+                }
+              }
+            ]
+          },
+          {
+            "sa": [
+              {
+                "meta": {
+                  "type": "map",
+                  "description": "Groovy Map containing sample information\ne.g. `[ id:'test', single_end:false ]`\n"
+                }
+              },
+              {
+                "*.sa": {
+                  "type": "file",
+                  "description": "Kaiju intermedite bwt-index file (not needed for classification)",
+                  "pattern": "*.{sa}"
+                }
+              }
+            ]
+          },
           {
             "versions": [
               {
@@ -99610,7 +99928,8 @@
           }
         ],
         "authors": [
-          "@alxndrdiaz"
+          "@alxndrdiaz",
+          "@jfy133"
         ]
       },
       "pipelines": [
@@ -102258,6 +102577,15 @@
                 "description": "custom seqid2taxid"
               }
             }
+          ],
+          [
+            {
+              "keep_intermediate": {
+                "type": "boolean",
+                "description": "Keep intermediate files",
+                "pattern": "true|false"
+              }
+            }
           ]
         ],
         "output": [
@@ -102270,7 +102598,7 @@
                 }
               },
               {
-                "$prefix/": {
+                "${prefix}/": {
                   "type": "directory",
                   "description": "Directory containing KrakenUniq database",
                   "pattern": "*/"
@@ -108905,6 +109233,22 @@
           "name": "pathogensurveillance",
           "version": "dev"
         },
+        {
+          "name": "phyloplace",
+          "version": "1.0.0"
+        },
+        {
+          "name": "ampliseq",
+          "version": "2.12.0"
+        },
+        {
+          "name": "multiplesequencealign",
+          "version": "1.0.0"
+        },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
         {
           "name": "phyloplace",
           "version": "1.0.0"
@@ -125043,7 +125387,7 @@
         },
         {
           "name": "rangeland",
-          "version": "dev"
+          "version": "1.0.0"
         },
         {
           "name": "raredisease",
@@ -134344,6 +134688,10 @@
           "name": "viralrecon",
           "version": "2.6.0"
         },
+        {
+          "name": "viralrecon",
+          "version": "2.6.0"
+        },
         {
           "name": "viralrecon",
           "version": "2.6.0"
@@ -192511,7 +192859,7 @@
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         {
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-          "version": "dev"
+          "version": "1.0.0"
         },
         {
           "name": "raredisease",
@@ -209576,6 +209924,10 @@
           "name": "phageannotator",
           "version": "dev"
         },
+        {
+          "name": "phageannotator",
+          "version": "dev"
+        },
         {
           "name": "phageannotator",
           "version": "dev"
@@ -213334,6 +213686,10 @@
           "name": "riboseq",
           "version": "1.0.1"
         },
+        {
+          "name": "riboseq",
+          "version": "1.0.1"
+        },
         {
           "name": "riboseq",
           "version": "1.0.1"
@@ -213808,7 +214164,7 @@
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         {
           "name": "rangeland",
-          "version": "dev"
+          "version": "1.0.0"
         },
         {
           "name": "raredisease",
@@ -214117,7 +214473,7 @@
         },
         {
           "name": "rangeland",
-          "version": "dev"
+          "version": "1.0.0"
         },
         {
           "name": "raredisease",
@@ -214328,6 +214684,10 @@
           "name": "mag",
           "version": "3.3.0"
         },
+        {
+          "name": "magmap",
+          "version": "dev"
+        },
         {
           "name": "mcmicro",
           "version": "dev"
@@ -214366,7 +214726,7 @@
         },
         {
           "name": "rangeland",
-          "version": "dev"
+          "version": "1.0.0"
         },
         {
           "name": "references",
@@ -214527,10 +214887,6 @@
           "name": "isoseq",
           "version": "2.0.0"
         },
-        {
-          "name": "magmap",
-          "version": "dev"
-        },
         {
           "name": "meerpipe",
           "version": "dev"
diff --git a/public/pipelines.json b/public/pipelines.json
index 155f54c468..88c3f38b80 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -1535,7 +1535,7 @@
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             "has_pages": false,
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+            "forks_count": 124,
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             "open_issues_count": 42,
@@ -1547,7 +1547,7 @@
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             ],
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-            "forks": 123,
+            "forks": 124,
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             "watchers": 195,
             "default_branch": "master",
@@ -1581,7 +1581,7 @@
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             },
-            "network_count": 123,
+            "network_count": 124,
             "subscribers_count": 150,
             "team_contributors_permission_push": true,
             "team_contributors_permission_admin": false,
@@ -5692,9 +5692,9 @@
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             "updated_at": "2025-01-13T19:21:37Z",
-            "pushed_at": "2025-01-14T09:47:16Z",
+            "pushed_at": "2025-01-17T10:40:30Z",
             "homepage": "https://nf-co.re/createtaxdb",
-            "size": 3232,
+            "size": 3255,
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@@ -5707,7 +5707,7 @@
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@@ -5721,7 +5721,7 @@
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@@ -5829,7 +5829,7 @@
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             "repository_url": "https://github.com/nf-core/createtaxdb",
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@@ -10755,7 +10755,7 @@
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@@ -10773,7 +10773,7 @@
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@@ -13366,12 +13366,12 @@
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             "created_at": "2021-06-03T09:26:41Z",
-            "updated_at": "2025-01-14T10:07:27Z",
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             "homepage": "https://nf-co.re/fetchngs",
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-            "stargazers_count": 156,
-            "watchers_count": 156,
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+            "watchers_count": 157,
             "language": "Nextflow",
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             "has_projects": true,
@@ -13398,7 +13398,7 @@
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             "open_issues": 33,
-            "watchers": 156,
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@@ -15010,10 +15010,10 @@
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-            "updated_at": "2025-01-16T15:38:55Z",
-            "pushed_at": "2025-01-16T15:39:07Z",
+            "updated_at": "2025-01-17T12:05:59Z",
+            "pushed_at": "2025-01-17T12:05:57Z",
             "homepage": "https://nf-co.re/genomeassembler",
-            "size": 4492,
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@@ -15136,7 +15136,7 @@
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@@ -15161,9 +15161,9 @@
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-            "head_sha": "548eb1cf5645fccf43a0b9645f8c4a367e2800b8",
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-            "last_release_vs_default_compare_url": "https://github.com/nf-core/genomeassembler/compare/548eb1cf5645fccf43a0b9645f8c4a367e2800b8...undefined",
+            "last_release_vs_default_compare_url": "https://github.com/nf-core/genomeassembler/compare/95a757717673a170e826eb149d5fca56f1cfe781...undefined",
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@@ -15181,8 +15181,8 @@
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-                    "published_at": "2025-01-16T15:38:40Z",
-                    "tag_sha": "548eb1cf5645fccf43a0b9645f8c4a367e2800b8",
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@@ -16106,12 +16106,12 @@
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             "created_at": "2019-04-09T14:29:19Z",
-            "updated_at": "2025-01-14T19:49:01Z",
+            "updated_at": "2025-01-17T10:59:51Z",
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             "homepage": "https://nf-co.re/hic",
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-            "stargazers_count": 94,
-            "watchers_count": 94,
+            "stargazers_count": 95,
+            "watchers_count": 95,
             "language": "Nextflow",
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             "has_projects": true,
@@ -16133,7 +16133,7 @@
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-            "watchers": 94,
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@@ -18911,7 +18911,7 @@
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@@ -18927,7 +18927,7 @@
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@@ -20622,14 +20622,14 @@
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