diff --git a/.cache.tar.xz b/.cache.tar.xz
index e143040f94..5b2ce6fb81 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index 7f25792bc1..3a64616cbf 100644
--- a/public/components.json
+++ b/public/components.json
@@ -8015,6 +8015,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -12241,7 +12245,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -17288,7 +17292,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -17490,7 +17494,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -26113,6 +26117,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -30012,7 +30024,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -32771,7 +32783,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -51914,7 +51926,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "taxprofiler",
@@ -53684,7 +53696,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "denovotranscript",
@@ -53901,7 +53913,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "denovotranscript",
@@ -57153,7 +57165,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -97676,7 +97688,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "detaxizer",
@@ -107192,7 +107204,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -109056,6 +109068,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -118316,7 +118332,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "denovotranscript",
@@ -150623,7 +150639,13 @@
         "maintainers": [
           "@nschcolnicov"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "demultiplex",
+          "version": "1.5.3"
+        }
+      ]
     },
     {
       "name": "samtools_ampliconclip",
@@ -161861,7 +161883,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "pathogensurveillance",
@@ -163440,7 +163462,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -183428,7 +183450,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "differentialabundance",
@@ -190793,6 +190815,444 @@
         ]
       }
     },
+    {
+      "name": "xeniumranger_import-segmentation",
+      "path": "modules/nf-core/xeniumranger/import-segmentation/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "xeniumranger_import_segmentation",
+        "description": "The xeniumranger import-segmentation module allows you to specify 2D nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation results can be generated by community-developed tools or prior Xenium segmentation result.",
+        "keywords": [
+          "spatial",
+          "segmentation",
+          "import segmentation",
+          "nuclear segmentation",
+          "cell segmentation",
+          "xeniumranger",
+          "imaging"
+        ],
+        "tools": [
+          {
+            "xeniumranger": {
+              "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n",
+              "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest",
+              "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started",
+              "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis",
+              "licence": [
+                "10x Genomics EULA"
+              ],
+              "identifier": ""
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing run information\ne.g. [id:'xenium_bundle_path']\n"
+              }
+            },
+            {
+              "xenium_bundle": {
+                "type": "directory",
+                "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline"
+              }
+            }
+          ],
+          [
+            {
+              "expansion_distance": {
+                "type": "integer",
+                "description": "Nuclei boundary expansion distance in µm. Only for use when nucleus segmentation provided as input. Default-5 (accepted range 0 - 100)"
+              }
+            }
+          ],
+          [
+            {
+              "coordinate_transform": {
+                "type": "file",
+                "description": "Image alignment file containing similarity transform matrix e.g., the _imagealignment.csv file exported from Xenium Explorer"
+              }
+            }
+          ],
+          [
+            {
+              "nuclei": {
+                "type": "file",
+                "description": "Label mask (TIFF or NPY), polygons of nucleus segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the nucleus masks as input).\n--nuclei will use nucleusGeometry polygon if it exists in the GeoJSON (i.e., for QuPath-like GeoJSON files),\nor geometry if it does not. Error if --transcript-assignment argument is used.\n"
+              }
+            }
+          ],
+          [
+            {
+              "cells": {
+                "type": "file",
+                "description": "Label mask (TIFF or NPY), polygons of cell segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the cell masks as input).\nFeatures with a non-cell objectType will be ignored. Error if --transcript-assignment argument is used.\nIn Xenium Ranger v2.0, --nuclei no longer needs to be used with --cells.\n"
+              }
+            }
+          ],
+          [
+            {
+              "transcript_assignment": {
+                "type": "file",
+                "description": "Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used.\n"
+              }
+            }
+          ],
+          [
+            {
+              "viz_polygons": {
+                "type": "file",
+                "description": "Cell boundary polygons (GeoJSON) for visualization from Baysor v0.6. Required if --transcript-assignment argument used. Error if --cells or --nuclei arguments used.\n"
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "outs": [
+              {
+                "meta": {
+                  "type": "file",
+                  "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              },
+              {
+                "**/outs/**": {
+                  "type": "file",
+                  "description": "Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@khersameesh24"
+        ],
+        "maintainers": [
+          "@khersameesh24"
+        ]
+      }
+    },
+    {
+      "name": "xeniumranger_relabel",
+      "path": "modules/nf-core/xeniumranger/relabel/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "xeniumranger_relabel",
+        "description": "The xeniumranger relabel module allows you to change the gene labels applied to decoded transcripts.",
+        "keywords": [
+          "spatial",
+          "relabel",
+          "gene labels",
+          "transcripts",
+          "xeniumranger"
+        ],
+        "tools": [
+          {
+            "xeniumranger": {
+              "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n",
+              "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest",
+              "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started",
+              "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis",
+              "licence": [
+                "10x Genomics EULA"
+              ],
+              "identifier": ""
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing run information\ne.g. [id:'xenium_bundle_path']\n"
+              }
+            },
+            {
+              "xenium_bundle": {
+                "type": "directory",
+                "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline"
+              }
+            }
+          ],
+          [
+            {
+              "gene_panel": {
+                "type": "file",
+                "description": "Gene panel JSON file to use for relabeling decoded transcripts"
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "outs": [
+              {
+                "meta": {
+                  "type": "file",
+                  "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              },
+              {
+                "**/outs/**": {
+                  "type": "file",
+                  "description": "Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@khersameesh24"
+        ],
+        "maintainers": [
+          "@khersameesh24"
+        ]
+      }
+    },
+    {
+      "name": "xeniumranger_rename",
+      "path": "modules/nf-core/xeniumranger/rename/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "xeniumranger_rename",
+        "description": "The xeniumranger rename module allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information.",
+        "keywords": [
+          "spatial",
+          "rename",
+          "gene labels",
+          "transcripts",
+          "xeniumranger"
+        ],
+        "tools": [
+          {
+            "xeniumranger": {
+              "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n",
+              "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest",
+              "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started",
+              "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis",
+              "licence": [
+                "10x Genomics EULA"
+              ],
+              "identifier": ""
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing sample information e.g. [ id:'test' ]"
+              }
+            },
+            {
+              "xenium_bundle": {
+                "type": "directory",
+                "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline"
+              }
+            }
+          ],
+          [
+            {
+              "region_name": {
+                "type": "string",
+                "description": "New region name"
+              }
+            }
+          ],
+          [
+            {
+              "cassette_name": {
+                "type": "string",
+                "description": "New cassette name"
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "outs": [
+              {
+                "meta": {
+                  "type": "file",
+                  "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              },
+              {
+                "**/outs/**": {
+                  "type": "file",
+                  "description": "Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@khersameesh24"
+        ],
+        "maintainers": [
+          "@khersameesh24"
+        ]
+      }
+    },
+    {
+      "name": "xeniumranger_resegment",
+      "path": "modules/nf-core/xeniumranger/resegment/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "xeniumranger_resegment",
+        "description": "The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.",
+        "keywords": [
+          "spatial",
+          "resegment",
+          "morphology",
+          "segmentation",
+          "xeniumranger"
+        ],
+        "tools": [
+          {
+            "xeniumranger": {
+              "description": "Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells.\n",
+              "homepage": "https://www.10xgenomics.com/support/software/xenium-ranger/latest",
+              "documentation": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started",
+              "tool_dev_url": "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis",
+              "licence": [
+                "10x Genomics EULA"
+              ],
+              "identifier": ""
+            }
+          }
+        ],
+        "input": [
+          [
+            {
+              "meta": {
+                "type": "map",
+                "description": "Groovy Map containing run information\ne.g. [ id:'xenium_experiment' ]\n"
+              }
+            },
+            {
+              "xenium_bundle": {
+                "type": "directory",
+                "description": "Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline"
+              }
+            }
+          ],
+          [
+            {
+              "expansion_distance": {
+                "type": "integer",
+                "description": "Nuclei boundary expansion distance in µm. Only for use when nucleus segmentation provided as input. Default-5 (accepted range 0 - 100)"
+              }
+            }
+          ],
+          [
+            {
+              "dapi_filter": {
+                "type": "integer",
+                "description": "Minimum intensity in photoelectrons to filter nuclei default-100 range of values is 0 to 99th percentile of image stack or 1000, whichever is larger"
+              }
+            }
+          ],
+          [
+            {
+              "boundary_stain": {
+                "type": "string",
+                "description": "Specify the name of the boundary stain to use or disable possible options are default-ATP1A1/CD45/E-Cadherin or disable"
+              }
+            }
+          ],
+          [
+            {
+              "interior_stain": {
+                "type": "string",
+                "description": "Specify the name of the interior stain to use or disable possible options are default-18S or disable"
+              }
+            }
+          ]
+        ],
+        "output": [
+          {
+            "outs": [
+              {
+                "meta": {
+                  "type": "file",
+                  "description": "Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              },
+              {
+                "**/outs/**": {
+                  "type": "file",
+                  "description": "Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs",
+                  "pattern": "${meta.id}/outs/*"
+                }
+              }
+            ]
+          },
+          {
+            "versions": [
+              {
+                "versions.yml": {
+                  "type": "file",
+                  "description": "File containing software versions",
+                  "pattern": "versions.yml"
+                }
+              }
+            ]
+          }
+        ],
+        "authors": [
+          "@khersameesh24"
+        ],
+        "maintainers": [
+          "@khersameesh24"
+        ]
+      }
+    },
     {
       "name": "xz_compress",
       "path": "modules/nf-core/xz/compress/meta.yml",
@@ -193923,7 +194383,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -196185,7 +196645,7 @@
       "pipelines": [
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         }
       ]
     },
@@ -201394,7 +201854,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "denovotranscript",
@@ -201675,7 +202135,7 @@
         },
         {
           "name": "demultiplex",
-          "version": "1.5.2"
+          "version": "1.5.3"
         },
         {
           "name": "denovotranscript",
@@ -201942,6 +202402,10 @@
           "name": "demo",
           "version": "1.0.1"
         },
+        {
+          "name": "demultiplex",
+          "version": "1.5.3"
+        },
         {
           "name": "fastqrepair",
           "version": "dev"
@@ -202101,10 +202565,6 @@
           "name": "datasync",
           "version": "dev"
         },
-        {
-          "name": "demultiplex",
-          "version": "1.5.2"
-        },
         {
           "name": "denovotranscript",
           "version": "1.0.0"
diff --git a/public/pipelines.json b/public/pipelines.json
index c95c077bb2..119c551532 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -2009,9 +2009,9 @@
             "url": "https://api.github.com/repos/nf-core/bacass",
             "created_at": "2019-01-31T08:03:31Z",
             "updated_at": "2024-09-05T12:48:42Z",
-            "pushed_at": "2024-11-05T13:48:55Z",
+            "pushed_at": "2024-11-06T08:45:01Z",
             "homepage": "https://nf-co.re/bacass",
-            "size": 5229,
+            "size": 5240,
             "stargazers_count": 60,
             "watchers_count": 60,
             "language": "Nextflow",
@@ -2416,8 +2416,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-11-05T13:48:55Z",
-                    "tag_sha": "067fb0f13eac6d46d18d642c6d585fc9cb00d425",
+                    "published_at": "2024-11-06T08:45:00Z",
+                    "tag_sha": "c476f50b0e95ea7c6aa7365b2fd532e957caf93e",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -4543,7 +4543,7 @@
             "forks_count": 22,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 19,
+            "open_issues_count": 20,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -4560,7 +4560,7 @@
             ],
             "visibility": "public",
             "forks": 22,
-            "open_issues": 19,
+            "open_issues": 20,
             "watchers": 44,
             "default_branch": "dev",
             "temp_clone_token": "",
@@ -7522,9 +7522,9 @@
             "url": "https://api.github.com/repos/nf-core/deepmodeloptim",
             "created_at": "2024-03-04T11:37:13Z",
             "updated_at": "2024-11-05T18:30:22Z",
-            "pushed_at": "2024-11-05T18:30:17Z",
+            "pushed_at": "2024-11-06T11:13:12Z",
             "homepage": "https://nf-co.re/deepmodeloptim",
-            "size": 2089,
+            "size": 2820,
             "stargazers_count": 23,
             "watchers_count": 23,
             "language": "Nextflow",
@@ -7534,10 +7534,10 @@
             "has_wiki": false,
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