diff --git a/doc/source/releases/25.1_announce.rst b/doc/source/releases/25.1_announce.rst
index 540f7dd83e9..714ec761e5d 100644
--- a/doc/source/releases/25.1_announce.rst
+++ b/doc/source/releases/25.1_announce.rst
@@ -1,6 +1,118 @@
 
-:orphan:
-
 ===========================================================
-25.1 Galaxy Release
+25.1 Galaxy Release (December 2025)
 ===========================================================
+
+.. include:: _header.rst
+
+Please see the `25.1 user release notes <25.1_announce_user.html>`__ for a summary of new user features.
+The `GitHub Release Notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ provide a comprehensive overview of all changes.
+
+Get Galaxy
+===========================================================
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_25.1 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_25.1 && git pull --ff-only origin release_25.1
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
+
+
+Admin Notes
+===========================================================
+
+**Database Migrations will require stopping the Galaxy instance**
+  This release includes database migrations that require the Galaxy instance to be stopped
+  before applying the update. Please plan accordingly to minimize downtime for users.
+
+Configuration Changes
+===========================================================
+
+
+Added
+-----
+
+The following configuration options are new
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.tool_shed.mapping.allow_local_account_creation
+
+
+Removed
+-------
+
+The following configuration options have been completely removed
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.tool_shed.mapping.allow_user_creation
+
+
+Deprecation Notices
+===========================================================
+
+**Deprecation of the Trackster Visualization in Galaxy release 26.0**
+  The legacy Trackster genome browser visualization has been deprecated and
+  `will be completely removed in Galaxy 26.0 <https://github.com/galaxyproject/galaxy/pull/20974>`__. This includes
+  the removal of special handling for Trackster across tool execution, toolbox filtering, visualization
+  framework features, controller endpoints, client code, and other conditional logic. With the removal of
+  Trackster, the era of Mako-based visualizations served from controller endpoints ends.
+  Galaxy now provides the modern IGV (Integrative Genomics Viewer) as the primary genome browser
+  visualization, offering superior functionality and performance for genomic data exploration.
+
+**Deprecation of Mako-based visualizations in Galaxy release 26.0**
+  With the removal of Trackster in 26.0, the remaining legacy Mako-based visualization framework
+  and controller endpoints are deprecated and
+  `will be completely removed in Galaxy 26.0 <https://github.com/galaxyproject/galaxy/pull/21133>`__.
+  Any remaining Mako-based visualizations should be migrated to the modern script-based visualization
+  plugin framework. Users and administrators are encouraged to transition to supported visualization
+  plugins to ensure continued functionality and access to new features.
+
+**Deprecation of the Galaxy Reports application in Galaxy release 26.0**
+  The standalone Galaxy Reports application, which provides administrative usage statistics and
+  analytics for Galaxy instances, is deprecated and will be removed in Galaxy 26.0.
+  The Reports app was a separate web application that connected to the Galaxy database to display
+  information about jobs, workflows, users, and system usage. Administrators currently using the
+  Reports app should plan to migrate to alternative monitoring and analytics solutions before
+  Galaxy 26.0 is released next year. The following GTN tutorials provide guidance on alternative
+  monitoring approaches:
+
+  * `Galaxy Monitoring with Telegraf and Grafana <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__
+  * `Galaxy Monitoring with gxadmin <https://training.galaxyproject.org/training-material/topics/admin/tutorials/gxadmin/tutorial.html>`__
+
+Release Team
+===========================================================
+
+Release manager:  `Ahmed Awan <https://github.com/ahmedhamidawan>`__, `Aysam Guerler <https://github.com/guerler>`__
+
+Release testing:
+
+* `Tyler Collins <https://github.com/tcollins2011>`__
+* `Arash Kadkhodaei <https://github.com/arash77>`__
+* `John Chilton <https://github.com/jmchilton>`__
+* `Keith Suderman <https://github.com/ksuderman>`__
+* `Aysam Guerler <https://github.com/guerler>`__
+* `Alireza Heidari <https://github.com/itisAliRH>`__
+* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__
+
+Communications:
+
+* `Natalie Whitaker-Allen <https://github.com/natalie-wa>`__
+* `Scott Cain <https://github.com/scottcain>`__
+
+A special thank you goes to everyone who helped test the new release after its deployment on usegalaxy.org.
+
+----
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/25.1_announce_user.rst b/doc/source/releases/25.1_announce_user.rst
new file mode 100644
index 00000000000..fec3e5865e0
--- /dev/null
+++ b/doc/source/releases/25.1_announce_user.rst
@@ -0,0 +1,456 @@
+
+===========================================================
+25.1 Galaxy Release (October 2025)
+===========================================================
+
+.. include:: _header.rst
+
+Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.
+
+Highlights
+===========================================================
+
+Discover some of the exciting new features, enhancements, and improvements in Galaxy 25.1.
+
+A Fresh, Modern History List Interface
+--------------------------------------
+
+Galaxy 25.1 introduces a redesigned history list that makes managing your histories more intuitive and
+visually appealing.
+
+- **Card-based design**. Histories are now displayed as clean, modern cards that provide better visual
+  organization in a grid vs list view, as you prefer.
+- **Enhanced information display**. Each history card shows key details at a glance, including 
+  creation date, size, update time, and status indicators in a more structured layout.
+- **Improved responsive design**. The new interface adapts better to different screen sizes and 
+  provides a more consistent experience across devices.
+- **Advanced keyboard navigation and selection**. Navigate through histories using arrow keys, 
+  select multiple histories with Shift+click for range selection, and use keyboard shortcuts 
+  for efficient bulk operations — available across multiple Galaxy list interfaces.
+
+This update modernizes one of Galaxy's core interfaces, providing a cleaner and more user-friendly 
+way to navigate your analysis history collection while adding powerful selection capabilities.
+[`#20744 <https://github.com/galaxyproject/galaxy/pull/20744>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/1kPTyiEr3ks?si=OYLxFeyA82bZ13Xd" title="Galaxy 25.1 - A Fresh, Modern History List Interface" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Smart Sample Sheets for Complex Workflow Inputs
+-----------------------------------------------
+
+Galaxy now supports **Sample Sheets** to simplify complex workflow inputs and data organization. This
+feature allows you to import data from external spreadsheets (CSV, TSV, or Excel) and use them to
+configure workflow parameters and organize datasets.
+
+- **Spreadsheet-style data entry**. Define your experimental data using familiar spreadsheet interfaces
+  with customizable columns for sample names, treatments, conditions, and file locations — whether
+  datasets or remote URLs.
+- **Workflow author-defined templates**. Workflow creators can pre-configure sample sheet templates
+  with specific columns, validation rules, and helpful descriptions, guiding users through proper data
+  organization.
+- **Built into the Apply Rules tool**. Advanced users can leverage sample sheet data within the Apply
+  Rules tool for sophisticated data manipulation and collection operations.
+- **Integration within the Workflow Editor**. Configure workflows to accept sample sheet inputs
+  directly from the Workflow Editor.
+
+Sample Sheets are particularly useful for workflows that require multiple related inputs or when you
+need to process batches of samples with associated metadata in a structured format.
+[`#19305 <https://github.com/galaxyproject/galaxy/pull/19305>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/5sAjEABPh8M?si=sxIX6RV1LtUkH4xW" title="Galaxy 25.1 - Smart Sample Sheets for Complex Workflow Inputs" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+An Enhanced Tool Discovery View
+-------------------------------
+
+Galaxy 25.1 introduces a redesigned **Tool Discovery View** that replaces the previous advanced tool
+search with a more powerful and intuitive tool exploration interface.
+
+- **Dedicated Discovery Interface**. Advanced tool search has moved from the tool panel to a rich,
+  dedicated center-panel view optimized for finding the right tools for your analysis.
+- **Card-based Tool Display**. Tools are presented as visually appealing cards with key information,
+  including EDAM ontology tags, descriptions, and links.
+- **Tool Favorites and Sharing**. Easily add tools to your favorites for quick access, and share useful
+  tools with colleagues via the copyable link feature.
+- **EDAM Ontology Integration**. Browse and filter tools by EDAM (EMBRACE Data and Methods) ontologies
+  to discover tools based on scientific domains and data types.
+
+This new interface makes tool discovery more efficient and helps users find the most appropriate tools
+for their specific analysis needs.
+[`#20747 <https://github.com/galaxyproject/galaxy/pull/20747>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/7L_QjcwyBiw?si=gD8tGTr0BTzgv7rw" title="Galaxy 25.1 - Tool Discovery View" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+New Galaxy Charts Visualization Framework
+-----------------------------------------
+
+This release also introduces the **Galaxy Charts** framework, bringing enhanced visualizations and a
+more powerful visualization experience to Galaxy users.
+
+- **Improved Visualization Performance**. Enjoy faster loading times, smoother interactions, and more
+  responsive visualizations built with modern web technologies for a better user experience.
+- **Enhanced IGV.js Genome Browser**. Galaxy now includes a complete IGV.js (Integrative Genome Browser)
+  integration for comprehensive genomic data visualization with multi-track support for BAM, VCF,
+  BigWig, BED, GFF, GTF, and CRAM files.
+- **Automatic Data Integration**. Visualizations now automatically connect to your Galaxy datasets and
+  match reference genomes, eliminating manual configuration steps and making it easier to explore your
+  data.
+- **Expanded Visualization Library**. The new framework enables rapid deployment of cutting-edge
+  visualizations, meaning Galaxy users will see more powerful visualization options in future releases.
+
+*See the Admin Notes and Deprecation Notices sections* :doc:`here <25.1_announce>` *for more details on
+the visualization framework and the removal of Trackster.*
+
+**Featured Implementation: IGV.js Genome Browser**
+
+Galaxy 25.1 ships with a complete IGV.js (Integrative Genome Browser) implementation built on the
+Galaxy Charts framework, showcasing the platform's capabilities:
+
+- **Multi-track Genomic Visualization**. View multiple tracks in various formats including BAM, VCF,
+  BigWig, BED, GFF, GTF, and CRAM files with full support for indexed data and byte-range requests.
+- **Automatic Genome Matching**. Automatically matches dataset database keys against available genomes,
+  supporting both IGV-provided reference genomes and Galaxy-served genomes in 2bit and FASTA formats.
+- **Interactive Exploration**. Full IGV.js functionality including zooming, panning, dynamic track
+  configuration, and multi-sample comparisons for comprehensive genomic data analysis.
+
+The Galaxy Charts framework represents a major advancement in Galaxy's visualization capabilities, 
+making it easier than ever to create sophisticated, interactive visualizations while maintaining full
+integration with Galaxy's data management and analysis ecosystem. Here's a look at the IGV.js addition:
+[`#20943 <https://github.com/galaxyproject/galaxy/pull/20943>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/VC05IvZGPiU?si=tMVdiHS1d5yTOX06" title="Galaxy 25.1 - New Galaxy Charts Visualization Framework" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+A Place to Find your Recent Downloads in Galaxy
+-----------------------------------------------
+
+Galaxy 25.1 introduces a dedicated "Recent Exports & Downloads" page that lists your recent
+exports/downloads.
+
+- **Re-download available items**. Easily access and download files still available in the short-term
+  storage cache.
+- **Navigate to source objects**. Jump directly to the details page of the originating item (e.g.
+  workflow invocation, history, etc.).
+
+This improves the discoverability and accessibility of recent downloads without needing to track links
+manually.
+[`#20585 <https://github.com/galaxyproject/galaxy/pull/20585>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/NMeH_HWuMwA?si=ly9gCTQksghLwRf0" title="Galaxy 25.1 - A Place to Find your Recent Downloads in Galaxy" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Visual Indicators for Short-Term Storage Expiration
+---------------------------------------------------
+
+Galaxy 25.1 introduces visual expiration indicators that help users identify when datasets and
+collections are stored in temporary or short-term storage that will be automatically cleaned up.
+
+- **Expiration warnings in history**. Datasets and collections now display countdown timers showing
+  when they will expire, helping users plan data management and downloads before automatic cleanup.
+- **Collection-aware indicators**. Smart detection across dataset collections shows the earliest
+  expiration time when collections contain datasets from mixed storage types.
+- **Admin-configurable expiration periods**. Administrators can set `object_expires_after_days` in
+  object store configurations to match their actual cleanup schedules and inform users appropriately.
+
+*Note that Galaxy instance administrators must set `object_expires_after_days` in their object store
+configurations for these indicators to function correctly.*
+
+This feature is particularly valuable for instances using scratch storage or temporary
+high-performance storage tiers, as it gives users clear visibility into data lifecycle and helps
+prevent unexpected data loss due to automatic cleanup processes.
+[`#20332 <https://github.com/galaxyproject/galaxy/pull/20332>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/CytCTixQTY8?si=taaSIrbl_gM2QhUC" title="Galaxy 25.1 - Visual Indicators for Short-Term Storage Expiration" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Galaxy Tools Now Handle Secrets and Authentication
+--------------------------------------------------
+
+Galaxy 25.1 implements a comprehensive tool credentials system, allowing tools to securely access
+external services by defining authentication credentials (variables and secrets) in tool requirements
+while keeping sensitive information separate from tool definitions.
+
+- **Credential Definition in Tools**. Tools can define credential requirements using `<credentials>`
+  elements within `<requirements>` with support for both variables (non-sensitive config like URLs,
+  usernames) and secrets (sensitive data like passwords, API keys).
+- **Secure Storage & Management**. Integration with Galaxy's vault system provides secure secret
+  storage with user-specific credential isolation by tool and service, plus credential groups for
+  organizing multiple credential sets.
+- **REST API**. Complete CRUD operations enable credential management with user credential listing,
+  group-based credential organization, and secure deletion with vault cleanup.
+- **Frontend Integration**. Unified credential management UI appears for every tool with workflow-level
+  credential status display, multi-tool credential coordination, and real-time credential validation
+  and feedback.
+- **Tool Execution Integration**. Automatic credential injection as environment variables with job
+  context tracking for credential usage, supporting tool proxies and various tool types while
+  maintaining backward compatibility.
+
+This system provides secure credential management for tools that need to access external APIs,
+databases, or cloud services, ensuring sensitive authentication information is properly protected
+while making it easy for users to configure and manage their credentials across different tools and
+workflows.
+[`#19084 <https://github.com/galaxyproject/galaxy/pull/19084>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/2xEFtTS3DSk?si=TvG5EUBy96Otrt9T" title="Galaxy 25.1 - Tools Now Handle Secrets and Authentication" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+Search for Steps, Tools and Subworkflows within the Workflow Editor
+-------------------------------------------------------------------
+
+As with many improvements to the Workflow Editor in recent releases, Galaxy 25.1 adds the ability to
+search for several properties of all elements in the workflow graph, displays the search results in a
+list, and highlights them when clicked.
+[`#20390 <https://github.com/galaxyproject/galaxy/pull/20390>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/Guma5nPqZ_8?si=BuQ2xkiCCULhV_Q5" title="Galaxy 25.1 - A Search in the Workflow Editor" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+A Redesign of your User Preferences
+-----------------------------------
+
+The User Preferences interface has been redesigned to enhance user experience through improved
+navigation and a modernised interface.
+[`#19658 <https://github.com/galaxyproject/galaxy/pull/19658>`__]
+
+.. raw:: html
+
+   <iframe width="100%" height="360" style="margin-bottom: 1em;" src="https://www.youtube.com/embed/vTjJtStlf9w?si=98P65gcBJP0xNDZA" title="Galaxy 25.1 - A Redesign of your User Preferences" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+----
+
+Visualizations Updates
+===========================================================
+
+.. visualizations
+* [igv] Allow selection of genomes from history fasta/2bit
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21269`_
+* Add Hyphy Vision Result Viewer
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21196`_
+* Enable drag-and-drop of collection elements in IGV
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21173`_
+* Update Javascript package licenses to MIT
+  (thanks to `@mr-c <https://github.com/mr-c>`__).
+  `Pull Request 20264`_
+* Install Visualization plugins as self-contained packages
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20348`_
+* Restore Nora
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20387`_
+* Install visualizations directly to static path, avoid duplication
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20372`_
+* Add rerun.io web viewer
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20202`_
+* Update tiffviewer visualization to version 0.0.3
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 20658`_
+* Consolidate visualization mako, avoid user agent styles
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20760`_
+* Enable data label column selection in basic Plotly plots and add heatmap
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20813`_
+* Update JupyterLite version to 0.6.4
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20877`_
+* Add Multiple Sequence Alignment Viewer 2.0
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20907`_
+* Make jupyterlite default visualization for ipynb
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20931`_
+* Fix JupyterLite History Identifier Retrieval Without Dataset
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20971`_
+* Save IGV locus and improve error handling
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20996`_
+* Bump vitessce to 3.8.2
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21003`_
+* Fix and migrate HIV-TRACE to Charts Visualization Framework
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21006`_
+* Add README and update the minimal visualization example
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21007`_
+* Allow creation of visualizations without dataset
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20914`_
+* Adds IGV.js Visualization
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 20943`_
+
+Datatypes Updates
+===========================================================
+
+.. datatypes
+* New datatype addition: HAL
+  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
+  `Pull Request 21379`_
+* Add PNTS datatype for 3D Tiles Point Cloud
+  (thanks to `@kgerb <https://github.com/kgerb>`__).
+  `Pull Request 21414`_
+* Backport fix anndata datatype update
+  (thanks to `@nilchia <https://github.com/nilchia>`__).
+  `Pull Request 21111`_
+* Fix MIME type for LAZ datatype
+  (thanks to `@kysrpex <https://github.com/kysrpex>`__).
+  `Pull Request 21202`_
+* Add SpatialData datatype
+  (thanks to `@nilchia <https://github.com/nilchia>`__).
+  `Pull Request 21000`_
+* support ZARR v3 for  Spatialdata dt
+  (thanks to `@nilchia <https://github.com/nilchia>`__).
+  `Pull Request 21265`_
+* Fix forward merge
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 21307`_
+* Fix tool-provided metadata for CONVERTER_tar_to_directory
+  (thanks to `@mr-c <https://github.com/mr-c>`__).
+  `Pull Request 20260`_
+* Pin isa-rwval 0.10.11, drop conditional import handling
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 20527`_
+* Remove ``num_unique_values`` tiff metadata element
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 20464`_
+* Add LocusZoom Visualization
+  (thanks to `@elmedjadjirayane <https://github.com/elmedjadjirayane>`__).
+  `Pull Request 20354`_
+* Add mzMLb and MBI datatypes
+  (thanks to `@chambm <https://github.com/chambm>`__).
+  `Pull Request 20632`_
+* Pairtool updated format and sniffers
+  (thanks to `@Smeds <https://github.com/Smeds>`__).
+  `Pull Request 20634`_
+* Add `num_unique_values` tiff metadata element, fixed
+  (thanks to `@kostrykin <https://github.com/kostrykin>`__).
+  `Pull Request 20669`_
+* add fasta.bz2 as auto_compressed type
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 20496`_
+* Add support for M4A audio files
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 20667`_
+* Add datatype for LexicMap index
+  (thanks to `@Smeds <https://github.com/Smeds>`__).
+  `Pull Request 20586`_
+* Bump requirement of directory converters
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 20834`_
+* Undo accidental push
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 20854`_
+* Fix Ipynb datatype sniffer and add unit tests
+  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
+  `Pull Request 20811`_
+* Add axt and maf to auto_compressed_types
+  (thanks to `@richard-burhans <https://github.com/richard-burhans>`__).
+  `Pull Request 20875`_
+* Add HiC datatype
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 20874`_
+* Fix DOCX detection and add PPTX support
+  (thanks to `@arash77 <https://github.com/arash77>`__).
+  `Pull Request 20827`_
+* Fix anndata metadata
+  (thanks to `@nilchia <https://github.com/nilchia>`__).
+  `Pull Request 20778`_
+* Use a streaming based parser (ijson) when setting metadata for biom1 files
+  (thanks to `@ksuderman <https://github.com/ksuderman>`__).
+  `Pull Request 20851`_
+* Add support for picking ``from_work_dir`` directory
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 20916`_
+* Skip sam metadata if we have too many references
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 20820`_
+* Extract: do not use common prefix dir
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 20929`_
+* Add Auspice JSON datatype
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 20466`_
+* Clean up code from pyupgrade
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 20642`_
+* Add safetensors datatype
+  (thanks to `@nilchia <https://github.com/nilchia>`__).
+  `Pull Request 20754`_
+* Add freq.json datatype subclass
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21012`_
+* Merge 25.0 into dev
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 21018`_
+* New datatype addition: beast.trees datatype
+  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
+  `Pull Request 21055`_
+* New datatype addition: gam for vg toolkit
+  (thanks to `@SaimMomin12 <https://github.com/SaimMomin12>`__).
+  `Pull Request 21096`_
+* Prefix download link
+  (thanks to `@martenson <https://github.com/martenson>`__).
+  `Pull Request 21112`_
+* Add LAS and LAZ file format
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 21049`_
+* Add display_in_upload to LAZ and LAS
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 21060`_
+* Type annotation fixes for mypy 1.16.0
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 20424`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Set minimum profile version for expression tools
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 21151`_
+* Drop ucsc test server from sample build sites
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 20723`_
+* Drop Python helper script from sort1 tool
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 20876`_
+* Update requirements of sort1 tool
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 20892`_
+* Update maf tools with profiles, required_files, and requirements
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 20865`_
+* Modernize tools in the filters/ dir
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 20840`_
+* Add special case for BAM files in RStudio
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 20692`_
+* Fix comp1 / test_subworkflow_map_over_data_column
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 20992`_
+
+Please see the full `release notes <https://github.com/galaxyproject/galaxy/releases/tag/v25.1.0>`__ for more details.
+The admin-facing release notes are available :doc:`here <25.1_announce>`.
+
+.. include:: 25.1_prs.rst
+
+----
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/25.1_prs.rst b/doc/source/releases/25.1_prs.rst
new file mode 100644
index 00000000000..208f4e0baaa
--- /dev/null
+++ b/doc/source/releases/25.1_prs.rst
@@ -0,0 +1,445 @@
+
+.. github_links
+.. _Pull Request 21442: https://github.com/galaxyproject/galaxy/pull/21442
+.. _Pull Request 21435: https://github.com/galaxyproject/galaxy/pull/21435
+.. _Pull Request 21342: https://github.com/galaxyproject/galaxy/pull/21342
+.. _Pull Request 21269: https://github.com/galaxyproject/galaxy/pull/21269
+.. _Pull Request 21346: https://github.com/galaxyproject/galaxy/pull/21346
+.. _Pull Request 21349: https://github.com/galaxyproject/galaxy/pull/21349
+.. _Pull Request 21350: https://github.com/galaxyproject/galaxy/pull/21350
+.. _Pull Request 21379: https://github.com/galaxyproject/galaxy/pull/21379
+.. _Pull Request 21276: https://github.com/galaxyproject/galaxy/pull/21276
+.. _Pull Request 21360: https://github.com/galaxyproject/galaxy/pull/21360
+.. _Pull Request 21377: https://github.com/galaxyproject/galaxy/pull/21377
+.. _Pull Request 21414: https://github.com/galaxyproject/galaxy/pull/21414
+.. _Pull Request 21419: https://github.com/galaxyproject/galaxy/pull/21419
+.. _Pull Request 21426: https://github.com/galaxyproject/galaxy/pull/21426
+.. _Pull Request 21428: https://github.com/galaxyproject/galaxy/pull/21428
+.. _Pull Request 21191: https://github.com/galaxyproject/galaxy/pull/21191
+.. _Pull Request 21193: https://github.com/galaxyproject/galaxy/pull/21193
+.. _Pull Request 21196: https://github.com/galaxyproject/galaxy/pull/21196
+.. _Pull Request 21195: https://github.com/galaxyproject/galaxy/pull/21195
+.. _Pull Request 21111: https://github.com/galaxyproject/galaxy/pull/21111
+.. _Pull Request 21202: https://github.com/galaxyproject/galaxy/pull/21202
+.. _Pull Request 21197: https://github.com/galaxyproject/galaxy/pull/21197
+.. _Pull Request 21192: https://github.com/galaxyproject/galaxy/pull/21192
+.. _Pull Request 21214: https://github.com/galaxyproject/galaxy/pull/21214
+.. _Pull Request 21203: https://github.com/galaxyproject/galaxy/pull/21203
+.. _Pull Request 21210: https://github.com/galaxyproject/galaxy/pull/21210
+.. _Pull Request 21212: https://github.com/galaxyproject/galaxy/pull/21212
+.. _Pull Request 21023: https://github.com/galaxyproject/galaxy/pull/21023
+.. _Pull Request 21223: https://github.com/galaxyproject/galaxy/pull/21223
+.. _Pull Request 21233: https://github.com/galaxyproject/galaxy/pull/21233
+.. _Pull Request 21213: https://github.com/galaxyproject/galaxy/pull/21213
+.. _Pull Request 21232: https://github.com/galaxyproject/galaxy/pull/21232
+.. _Pull Request 21000: https://github.com/galaxyproject/galaxy/pull/21000
+.. _Pull Request 21246: https://github.com/galaxyproject/galaxy/pull/21246
+.. _Pull Request 21240: https://github.com/galaxyproject/galaxy/pull/21240
+.. _Pull Request 21249: https://github.com/galaxyproject/galaxy/pull/21249
+.. _Pull Request 21200: https://github.com/galaxyproject/galaxy/pull/21200
+.. _Pull Request 21274: https://github.com/galaxyproject/galaxy/pull/21274
+.. _Pull Request 21265: https://github.com/galaxyproject/galaxy/pull/21265
+.. _Pull Request 21282: https://github.com/galaxyproject/galaxy/pull/21282
+.. _Pull Request 21284: https://github.com/galaxyproject/galaxy/pull/21284
+.. _Pull Request 21280: https://github.com/galaxyproject/galaxy/pull/21280
+.. _Pull Request 21293: https://github.com/galaxyproject/galaxy/pull/21293
+.. _Pull Request 21013: https://github.com/galaxyproject/galaxy/pull/21013
+.. _Pull Request 21290: https://github.com/galaxyproject/galaxy/pull/21290
+.. _Pull Request 21294: https://github.com/galaxyproject/galaxy/pull/21294
+.. _Pull Request 21314: https://github.com/galaxyproject/galaxy/pull/21314
+.. _Pull Request 21307: https://github.com/galaxyproject/galaxy/pull/21307
+.. _Pull Request 21261: https://github.com/galaxyproject/galaxy/pull/21261
+.. _Pull Request 21273: https://github.com/galaxyproject/galaxy/pull/21273
+.. _Pull Request 21286: https://github.com/galaxyproject/galaxy/pull/21286
+.. _Pull Request 21185: https://github.com/galaxyproject/galaxy/pull/21185
+.. _Pull Request 21184: https://github.com/galaxyproject/galaxy/pull/21184
+.. _Pull Request 21175: https://github.com/galaxyproject/galaxy/pull/21175
+.. _Pull Request 21181: https://github.com/galaxyproject/galaxy/pull/21181
+.. _Pull Request 21159: https://github.com/galaxyproject/galaxy/pull/21159
+.. _Pull Request 21166: https://github.com/galaxyproject/galaxy/pull/21166
+.. _Pull Request 21165: https://github.com/galaxyproject/galaxy/pull/21165
+.. _Pull Request 21164: https://github.com/galaxyproject/galaxy/pull/21164
+.. _Pull Request 21160: https://github.com/galaxyproject/galaxy/pull/21160
+.. _Pull Request 21169: https://github.com/galaxyproject/galaxy/pull/21169
+.. _Pull Request 21173: https://github.com/galaxyproject/galaxy/pull/21173
+.. _Pull Request 21085: https://github.com/galaxyproject/galaxy/pull/21085
+.. _Pull Request 21151: https://github.com/galaxyproject/galaxy/pull/21151
+.. _Pull Request 21156: https://github.com/galaxyproject/galaxy/pull/21156
+.. _Pull Request 20260: https://github.com/galaxyproject/galaxy/pull/20260
+.. _Pull Request 20268: https://github.com/galaxyproject/galaxy/pull/20268
+.. _Pull Request 20264: https://github.com/galaxyproject/galaxy/pull/20264
+.. _Pull Request 20278: https://github.com/galaxyproject/galaxy/pull/20278
+.. _Pull Request 20262: https://github.com/galaxyproject/galaxy/pull/20262
+.. _Pull Request 20284: https://github.com/galaxyproject/galaxy/pull/20284
+.. _Pull Request 20292: https://github.com/galaxyproject/galaxy/pull/20292
+.. _Pull Request 20291: https://github.com/galaxyproject/galaxy/pull/20291
+.. _Pull Request 20139: https://github.com/galaxyproject/galaxy/pull/20139
+.. _Pull Request 20347: https://github.com/galaxyproject/galaxy/pull/20347
+.. _Pull Request 20348: https://github.com/galaxyproject/galaxy/pull/20348
+.. _Pull Request 20355: https://github.com/galaxyproject/galaxy/pull/20355
+.. _Pull Request 20364: https://github.com/galaxyproject/galaxy/pull/20364
+.. _Pull Request 20408: https://github.com/galaxyproject/galaxy/pull/20408
+.. _Pull Request 20303: https://github.com/galaxyproject/galaxy/pull/20303
+.. _Pull Request 20422: https://github.com/galaxyproject/galaxy/pull/20422
+.. _Pull Request 20356: https://github.com/galaxyproject/galaxy/pull/20356
+.. _Pull Request 20357: https://github.com/galaxyproject/galaxy/pull/20357
+.. _Pull Request 20445: https://github.com/galaxyproject/galaxy/pull/20445
+.. _Pull Request 20446: https://github.com/galaxyproject/galaxy/pull/20446
+.. _Pull Request 20435: https://github.com/galaxyproject/galaxy/pull/20435
+.. _Pull Request 20387: https://github.com/galaxyproject/galaxy/pull/20387
+.. _Pull Request 20418: https://github.com/galaxyproject/galaxy/pull/20418
+.. _Pull Request 20383: https://github.com/galaxyproject/galaxy/pull/20383
+.. _Pull Request 20470: https://github.com/galaxyproject/galaxy/pull/20470
+.. _Pull Request 20372: https://github.com/galaxyproject/galaxy/pull/20372
+.. _Pull Request 20500: https://github.com/galaxyproject/galaxy/pull/20500
+.. _Pull Request 20501: https://github.com/galaxyproject/galaxy/pull/20501
+.. _Pull Request 20507: https://github.com/galaxyproject/galaxy/pull/20507
+.. _Pull Request 20509: https://github.com/galaxyproject/galaxy/pull/20509
+.. _Pull Request 20520: https://github.com/galaxyproject/galaxy/pull/20520
+.. _Pull Request 20516: https://github.com/galaxyproject/galaxy/pull/20516
+.. _Pull Request 20526: https://github.com/galaxyproject/galaxy/pull/20526
+.. _Pull Request 20527: https://github.com/galaxyproject/galaxy/pull/20527
+.. _Pull Request 20531: https://github.com/galaxyproject/galaxy/pull/20531
+.. _Pull Request 20529: https://github.com/galaxyproject/galaxy/pull/20529
+.. _Pull Request 20438: https://github.com/galaxyproject/galaxy/pull/20438
+.. _Pull Request 20511: https://github.com/galaxyproject/galaxy/pull/20511
+.. _Pull Request 20528: https://github.com/galaxyproject/galaxy/pull/20528
+.. _Pull Request 20518: https://github.com/galaxyproject/galaxy/pull/20518
+.. _Pull Request 20533: https://github.com/galaxyproject/galaxy/pull/20533
+.. _Pull Request 20534: https://github.com/galaxyproject/galaxy/pull/20534
+.. _Pull Request 20464: https://github.com/galaxyproject/galaxy/pull/20464
+.. _Pull Request 20536: https://github.com/galaxyproject/galaxy/pull/20536
+.. _Pull Request 20545: https://github.com/galaxyproject/galaxy/pull/20545
+.. _Pull Request 20354: https://github.com/galaxyproject/galaxy/pull/20354
+.. _Pull Request 20552: https://github.com/galaxyproject/galaxy/pull/20552
+.. _Pull Request 20525: https://github.com/galaxyproject/galaxy/pull/20525
+.. _Pull Request 20546: https://github.com/galaxyproject/galaxy/pull/20546
+.. _Pull Request 20537: https://github.com/galaxyproject/galaxy/pull/20537
+.. _Pull Request 20497: https://github.com/galaxyproject/galaxy/pull/20497
+.. _Pull Request 20577: https://github.com/galaxyproject/galaxy/pull/20577
+.. _Pull Request 20571: https://github.com/galaxyproject/galaxy/pull/20571
+.. _Pull Request 20584: https://github.com/galaxyproject/galaxy/pull/20584
+.. _Pull Request 20502: https://github.com/galaxyproject/galaxy/pull/20502
+.. _Pull Request 20591: https://github.com/galaxyproject/galaxy/pull/20591
+.. _Pull Request 20202: https://github.com/galaxyproject/galaxy/pull/20202
+.. _Pull Request 20593: https://github.com/galaxyproject/galaxy/pull/20593
+.. _Pull Request 20596: https://github.com/galaxyproject/galaxy/pull/20596
+.. _Pull Request 20601: https://github.com/galaxyproject/galaxy/pull/20601
+.. _Pull Request 20597: https://github.com/galaxyproject/galaxy/pull/20597
+.. _Pull Request 20594: https://github.com/galaxyproject/galaxy/pull/20594
+.. _Pull Request 20603: https://github.com/galaxyproject/galaxy/pull/20603
+.. _Pull Request 20460: https://github.com/galaxyproject/galaxy/pull/20460
+.. _Pull Request 20618: https://github.com/galaxyproject/galaxy/pull/20618
+.. _Pull Request 20521: https://github.com/galaxyproject/galaxy/pull/20521
+.. _Pull Request 20625: https://github.com/galaxyproject/galaxy/pull/20625
+.. _Pull Request 20615: https://github.com/galaxyproject/galaxy/pull/20615
+.. _Pull Request 20636: https://github.com/galaxyproject/galaxy/pull/20636
+.. _Pull Request 20632: https://github.com/galaxyproject/galaxy/pull/20632
+.. _Pull Request 20620: https://github.com/galaxyproject/galaxy/pull/20620
+.. _Pull Request 20639: https://github.com/galaxyproject/galaxy/pull/20639
+.. _Pull Request 20551: https://github.com/galaxyproject/galaxy/pull/20551
+.. _Pull Request 19697: https://github.com/galaxyproject/galaxy/pull/19697
+.. _Pull Request 20646: https://github.com/galaxyproject/galaxy/pull/20646
+.. _Pull Request 20638: https://github.com/galaxyproject/galaxy/pull/20638
+.. _Pull Request 20627: https://github.com/galaxyproject/galaxy/pull/20627
+.. _Pull Request 20651: https://github.com/galaxyproject/galaxy/pull/20651
+.. _Pull Request 20654: https://github.com/galaxyproject/galaxy/pull/20654
+.. _Pull Request 20649: https://github.com/galaxyproject/galaxy/pull/20649
+.. _Pull Request 20658: https://github.com/galaxyproject/galaxy/pull/20658
+.. _Pull Request 20652: https://github.com/galaxyproject/galaxy/pull/20652
+.. _Pull Request 20647: https://github.com/galaxyproject/galaxy/pull/20647
+.. _Pull Request 20653: https://github.com/galaxyproject/galaxy/pull/20653
+.. _Pull Request 20663: https://github.com/galaxyproject/galaxy/pull/20663
+.. _Pull Request 20665: https://github.com/galaxyproject/galaxy/pull/20665
+.. _Pull Request 20630: https://github.com/galaxyproject/galaxy/pull/20630
+.. _Pull Request 20664: https://github.com/galaxyproject/galaxy/pull/20664
+.. _Pull Request 20634: https://github.com/galaxyproject/galaxy/pull/20634
+.. _Pull Request 20669: https://github.com/galaxyproject/galaxy/pull/20669
+.. _Pull Request 20547: https://github.com/galaxyproject/galaxy/pull/20547
+.. _Pull Request 20672: https://github.com/galaxyproject/galaxy/pull/20672
+.. _Pull Request 20674: https://github.com/galaxyproject/galaxy/pull/20674
+.. _Pull Request 20496: https://github.com/galaxyproject/galaxy/pull/20496
+.. _Pull Request 20667: https://github.com/galaxyproject/galaxy/pull/20667
+.. _Pull Request 20680: https://github.com/galaxyproject/galaxy/pull/20680
+.. _Pull Request 20685: https://github.com/galaxyproject/galaxy/pull/20685
+.. _Pull Request 20690: https://github.com/galaxyproject/galaxy/pull/20690
+.. _Pull Request 20693: https://github.com/galaxyproject/galaxy/pull/20693
+.. _Pull Request 20696: https://github.com/galaxyproject/galaxy/pull/20696
+.. _Pull Request 20699: https://github.com/galaxyproject/galaxy/pull/20699
+.. _Pull Request 20694: https://github.com/galaxyproject/galaxy/pull/20694
+.. _Pull Request 20702: https://github.com/galaxyproject/galaxy/pull/20702
+.. _Pull Request 20586: https://github.com/galaxyproject/galaxy/pull/20586
+.. _Pull Request 20553: https://github.com/galaxyproject/galaxy/pull/20553
+.. _Pull Request 20703: https://github.com/galaxyproject/galaxy/pull/20703
+.. _Pull Request 20510: https://github.com/galaxyproject/galaxy/pull/20510
+.. _Pull Request 20684: https://github.com/galaxyproject/galaxy/pull/20684
+.. _Pull Request 20708: https://github.com/galaxyproject/galaxy/pull/20708
+.. _Pull Request 20522: https://github.com/galaxyproject/galaxy/pull/20522
+.. _Pull Request 20705: https://github.com/galaxyproject/galaxy/pull/20705
+.. _Pull Request 20729: https://github.com/galaxyproject/galaxy/pull/20729
+.. _Pull Request 20723: https://github.com/galaxyproject/galaxy/pull/20723
+.. _Pull Request 20721: https://github.com/galaxyproject/galaxy/pull/20721
+.. _Pull Request 20714: https://github.com/galaxyproject/galaxy/pull/20714
+.. _Pull Request 20732: https://github.com/galaxyproject/galaxy/pull/20732
+.. _Pull Request 20734: https://github.com/galaxyproject/galaxy/pull/20734
+.. _Pull Request 20727: https://github.com/galaxyproject/galaxy/pull/20727
+.. _Pull Request 20739: https://github.com/galaxyproject/galaxy/pull/20739
+.. _Pull Request 20753: https://github.com/galaxyproject/galaxy/pull/20753
+.. _Pull Request 20752: https://github.com/galaxyproject/galaxy/pull/20752
+.. _Pull Request 20755: https://github.com/galaxyproject/galaxy/pull/20755
+.. _Pull Request 20710: https://github.com/galaxyproject/galaxy/pull/20710
+.. _Pull Request 20760: https://github.com/galaxyproject/galaxy/pull/20760
+.. _Pull Request 20701: https://github.com/galaxyproject/galaxy/pull/20701
+.. _Pull Request 20736: https://github.com/galaxyproject/galaxy/pull/20736
+.. _Pull Request 20731: https://github.com/galaxyproject/galaxy/pull/20731
+.. _Pull Request 20762: https://github.com/galaxyproject/galaxy/pull/20762
+.. _Pull Request 20772: https://github.com/galaxyproject/galaxy/pull/20772
+.. _Pull Request 20769: https://github.com/galaxyproject/galaxy/pull/20769
+.. _Pull Request 20770: https://github.com/galaxyproject/galaxy/pull/20770
+.. _Pull Request 20775: https://github.com/galaxyproject/galaxy/pull/20775
+.. _Pull Request 20768: https://github.com/galaxyproject/galaxy/pull/20768
+.. _Pull Request 20779: https://github.com/galaxyproject/galaxy/pull/20779
+.. _Pull Request 20777: https://github.com/galaxyproject/galaxy/pull/20777
+.. _Pull Request 20749: https://github.com/galaxyproject/galaxy/pull/20749
+.. _Pull Request 20384: https://github.com/galaxyproject/galaxy/pull/20384
+.. _Pull Request 20402: https://github.com/galaxyproject/galaxy/pull/20402
+.. _Pull Request 20782: https://github.com/galaxyproject/galaxy/pull/20782
+.. _Pull Request 20784: https://github.com/galaxyproject/galaxy/pull/20784
+.. _Pull Request 20728: https://github.com/galaxyproject/galaxy/pull/20728
+.. _Pull Request 20698: https://github.com/galaxyproject/galaxy/pull/20698
+.. _Pull Request 20783: https://github.com/galaxyproject/galaxy/pull/20783
+.. _Pull Request 20795: https://github.com/galaxyproject/galaxy/pull/20795
+.. _Pull Request 20786: https://github.com/galaxyproject/galaxy/pull/20786
+.. _Pull Request 20806: https://github.com/galaxyproject/galaxy/pull/20806
+.. _Pull Request 20812: https://github.com/galaxyproject/galaxy/pull/20812
+.. _Pull Request 20807: https://github.com/galaxyproject/galaxy/pull/20807
+.. _Pull Request 20813: https://github.com/galaxyproject/galaxy/pull/20813
+.. _Pull Request 20814: https://github.com/galaxyproject/galaxy/pull/20814
+.. _Pull Request 20799: https://github.com/galaxyproject/galaxy/pull/20799
+.. _Pull Request 20794: https://github.com/galaxyproject/galaxy/pull/20794
+.. _Pull Request 20800: https://github.com/galaxyproject/galaxy/pull/20800
+.. _Pull Request 20774: https://github.com/galaxyproject/galaxy/pull/20774
+.. _Pull Request 20822: https://github.com/galaxyproject/galaxy/pull/20822
+.. _Pull Request 20771: https://github.com/galaxyproject/galaxy/pull/20771
+.. _Pull Request 20823: https://github.com/galaxyproject/galaxy/pull/20823
+.. _Pull Request 20824: https://github.com/galaxyproject/galaxy/pull/20824
+.. _Pull Request 20829: https://github.com/galaxyproject/galaxy/pull/20829
+.. _Pull Request 20834: https://github.com/galaxyproject/galaxy/pull/20834
+.. _Pull Request 20797: https://github.com/galaxyproject/galaxy/pull/20797
+.. _Pull Request 20836: https://github.com/galaxyproject/galaxy/pull/20836
+.. _Pull Request 20837: https://github.com/galaxyproject/galaxy/pull/20837
+.. _Pull Request 20841: https://github.com/galaxyproject/galaxy/pull/20841
+.. _Pull Request 20761: https://github.com/galaxyproject/galaxy/pull/20761
+.. _Pull Request 20854: https://github.com/galaxyproject/galaxy/pull/20854
+.. _Pull Request 20866: https://github.com/galaxyproject/galaxy/pull/20866
+.. _Pull Request 20811: https://github.com/galaxyproject/galaxy/pull/20811
+.. _Pull Request 20869: https://github.com/galaxyproject/galaxy/pull/20869
+.. _Pull Request 20863: https://github.com/galaxyproject/galaxy/pull/20863
+.. _Pull Request 20871: https://github.com/galaxyproject/galaxy/pull/20871
+.. _Pull Request 20873: https://github.com/galaxyproject/galaxy/pull/20873
+.. _Pull Request 20853: https://github.com/galaxyproject/galaxy/pull/20853
+.. _Pull Request 20859: https://github.com/galaxyproject/galaxy/pull/20859
+.. _Pull Request 20872: https://github.com/galaxyproject/galaxy/pull/20872
+.. _Pull Request 20870: https://github.com/galaxyproject/galaxy/pull/20870
+.. _Pull Request 20877: https://github.com/galaxyproject/galaxy/pull/20877
+.. _Pull Request 20875: https://github.com/galaxyproject/galaxy/pull/20875
+.. _Pull Request 20874: https://github.com/galaxyproject/galaxy/pull/20874
+.. _Pull Request 20884: https://github.com/galaxyproject/galaxy/pull/20884
+.. _Pull Request 20889: https://github.com/galaxyproject/galaxy/pull/20889
+.. _Pull Request 20888: https://github.com/galaxyproject/galaxy/pull/20888
+.. _Pull Request 20886: https://github.com/galaxyproject/galaxy/pull/20886
+.. _Pull Request 20891: https://github.com/galaxyproject/galaxy/pull/20891
+.. _Pull Request 20876: https://github.com/galaxyproject/galaxy/pull/20876
+.. _Pull Request 20892: https://github.com/galaxyproject/galaxy/pull/20892
+.. _Pull Request 20887: https://github.com/galaxyproject/galaxy/pull/20887
+.. _Pull Request 20890: https://github.com/galaxyproject/galaxy/pull/20890
+.. _Pull Request 20880: https://github.com/galaxyproject/galaxy/pull/20880
+.. _Pull Request 20893: https://github.com/galaxyproject/galaxy/pull/20893
+.. _Pull Request 20895: https://github.com/galaxyproject/galaxy/pull/20895
+.. _Pull Request 20827: https://github.com/galaxyproject/galaxy/pull/20827
+.. _Pull Request 20905: https://github.com/galaxyproject/galaxy/pull/20905
+.. _Pull Request 20862: https://github.com/galaxyproject/galaxy/pull/20862
+.. _Pull Request 20908: https://github.com/galaxyproject/galaxy/pull/20908
+.. _Pull Request 20907: https://github.com/galaxyproject/galaxy/pull/20907
+.. _Pull Request 20778: https://github.com/galaxyproject/galaxy/pull/20778
+.. _Pull Request 20332: https://github.com/galaxyproject/galaxy/pull/20332
+.. _Pull Request 20909: https://github.com/galaxyproject/galaxy/pull/20909
+.. _Pull Request 20650: https://github.com/galaxyproject/galaxy/pull/20650
+.. _Pull Request 20915: https://github.com/galaxyproject/galaxy/pull/20915
+.. _Pull Request 20920: https://github.com/galaxyproject/galaxy/pull/20920
+.. _Pull Request 20918: https://github.com/galaxyproject/galaxy/pull/20918
+.. _Pull Request 20919: https://github.com/galaxyproject/galaxy/pull/20919
+.. _Pull Request 20922: https://github.com/galaxyproject/galaxy/pull/20922
+.. _Pull Request 20921: https://github.com/galaxyproject/galaxy/pull/20921
+.. _Pull Request 20917: https://github.com/galaxyproject/galaxy/pull/20917
+.. _Pull Request 20925: https://github.com/galaxyproject/galaxy/pull/20925
+.. _Pull Request 20930: https://github.com/galaxyproject/galaxy/pull/20930
+.. _Pull Request 20928: https://github.com/galaxyproject/galaxy/pull/20928
+.. _Pull Request 20932: https://github.com/galaxyproject/galaxy/pull/20932
+.. _Pull Request 20941: https://github.com/galaxyproject/galaxy/pull/20941
+.. _Pull Request 20939: https://github.com/galaxyproject/galaxy/pull/20939
+.. _Pull Request 20938: https://github.com/galaxyproject/galaxy/pull/20938
+.. _Pull Request 20937: https://github.com/galaxyproject/galaxy/pull/20937
+.. _Pull Request 20942: https://github.com/galaxyproject/galaxy/pull/20942
+.. _Pull Request 19086: https://github.com/galaxyproject/galaxy/pull/19086
+.. _Pull Request 20838: https://github.com/galaxyproject/galaxy/pull/20838
+.. _Pull Request 20361: https://github.com/galaxyproject/galaxy/pull/20361
+.. _Pull Request 20940: https://github.com/galaxyproject/galaxy/pull/20940
+.. _Pull Request 18732: https://github.com/galaxyproject/galaxy/pull/18732
+.. _Pull Request 20899: https://github.com/galaxyproject/galaxy/pull/20899
+.. _Pull Request 20717: https://github.com/galaxyproject/galaxy/pull/20717
+.. _Pull Request 20946: https://github.com/galaxyproject/galaxy/pull/20946
+.. _Pull Request 20951: https://github.com/galaxyproject/galaxy/pull/20951
+.. _Pull Request 20851: https://github.com/galaxyproject/galaxy/pull/20851
+.. _Pull Request 20945: https://github.com/galaxyproject/galaxy/pull/20945
+.. _Pull Request 20865: https://github.com/galaxyproject/galaxy/pull/20865
+.. _Pull Request 20957: https://github.com/galaxyproject/galaxy/pull/20957
+.. _Pull Request 20962: https://github.com/galaxyproject/galaxy/pull/20962
+.. _Pull Request 20965: https://github.com/galaxyproject/galaxy/pull/20965
+.. _Pull Request 20718: https://github.com/galaxyproject/galaxy/pull/20718
+.. _Pull Request 20963: https://github.com/galaxyproject/galaxy/pull/20963
+.. _Pull Request 20975: https://github.com/galaxyproject/galaxy/pull/20975
+.. _Pull Request 20949: https://github.com/galaxyproject/galaxy/pull/20949
+.. _Pull Request 20954: https://github.com/galaxyproject/galaxy/pull/20954
+.. _Pull Request 20906: https://github.com/galaxyproject/galaxy/pull/20906
+.. _Pull Request 20885: https://github.com/galaxyproject/galaxy/pull/20885
+.. _Pull Request 20707: https://github.com/galaxyproject/galaxy/pull/20707
+.. _Pull Request 20828: https://github.com/galaxyproject/galaxy/pull/20828
+.. _Pull Request 20931: https://github.com/galaxyproject/galaxy/pull/20931
+.. _Pull Request 20960: https://github.com/galaxyproject/galaxy/pull/20960
+.. _Pull Request 20980: https://github.com/galaxyproject/galaxy/pull/20980
+.. _Pull Request 20926: https://github.com/galaxyproject/galaxy/pull/20926
+.. _Pull Request 20916: https://github.com/galaxyproject/galaxy/pull/20916
+.. _Pull Request 20840: https://github.com/galaxyproject/galaxy/pull/20840
+.. _Pull Request 20830: https://github.com/galaxyproject/galaxy/pull/20830
+.. _Pull Request 20820: https://github.com/galaxyproject/galaxy/pull/20820
+.. _Pull Request 20177: https://github.com/galaxyproject/galaxy/pull/20177
+.. _Pull Request 19817: https://github.com/galaxyproject/galaxy/pull/19817
+.. _Pull Request 20929: https://github.com/galaxyproject/galaxy/pull/20929
+.. _Pull Request 20466: https://github.com/galaxyproject/galaxy/pull/20466
+.. _Pull Request 20692: https://github.com/galaxyproject/galaxy/pull/20692
+.. _Pull Request 20986: https://github.com/galaxyproject/galaxy/pull/20986
+.. _Pull Request 13570: https://github.com/galaxyproject/galaxy/pull/13570
+.. _Pull Request 20519: https://github.com/galaxyproject/galaxy/pull/20519
+.. _Pull Request 20523: https://github.com/galaxyproject/galaxy/pull/20523
+.. _Pull Request 20524: https://github.com/galaxyproject/galaxy/pull/20524
+.. _Pull Request 20542: https://github.com/galaxyproject/galaxy/pull/20542
+.. _Pull Request 20566: https://github.com/galaxyproject/galaxy/pull/20566
+.. _Pull Request 20575: https://github.com/galaxyproject/galaxy/pull/20575
+.. _Pull Request 20582: https://github.com/galaxyproject/galaxy/pull/20582
+.. _Pull Request 20599: https://github.com/galaxyproject/galaxy/pull/20599
+.. _Pull Request 20656: https://github.com/galaxyproject/galaxy/pull/20656
+.. _Pull Request 20676: https://github.com/galaxyproject/galaxy/pull/20676
+.. _Pull Request 20713: https://github.com/galaxyproject/galaxy/pull/20713
+.. _Pull Request 20780: https://github.com/galaxyproject/galaxy/pull/20780
+.. _Pull Request 20856: https://github.com/galaxyproject/galaxy/pull/20856
+.. _Pull Request 20883: https://github.com/galaxyproject/galaxy/pull/20883
+.. _Pull Request 20936: https://github.com/galaxyproject/galaxy/pull/20936
+.. _Pull Request 20953: https://github.com/galaxyproject/galaxy/pull/20953
+.. _Pull Request 20968: https://github.com/galaxyproject/galaxy/pull/20968
+.. _Pull Request 20970: https://github.com/galaxyproject/galaxy/pull/20970
+.. _Pull Request 20976: https://github.com/galaxyproject/galaxy/pull/20976
+.. _Pull Request 20982: https://github.com/galaxyproject/galaxy/pull/20982
+.. _Pull Request 20983: https://github.com/galaxyproject/galaxy/pull/20983
+.. _Pull Request 20984: https://github.com/galaxyproject/galaxy/pull/20984
+.. _Pull Request 20844: https://github.com/galaxyproject/galaxy/pull/20844
+.. _Pull Request 20994: https://github.com/galaxyproject/galaxy/pull/20994
+.. _Pull Request 20971: https://github.com/galaxyproject/galaxy/pull/20971
+.. _Pull Request 20662: https://github.com/galaxyproject/galaxy/pull/20662
+.. _Pull Request 20576: https://github.com/galaxyproject/galaxy/pull/20576
+.. _Pull Request 20626: https://github.com/galaxyproject/galaxy/pull/20626
+.. _Pull Request 20815: https://github.com/galaxyproject/galaxy/pull/20815
+.. _Pull Request 20845: https://github.com/galaxyproject/galaxy/pull/20845
+.. _Pull Request 20992: https://github.com/galaxyproject/galaxy/pull/20992
+.. _Pull Request 20826: https://github.com/galaxyproject/galaxy/pull/20826
+.. _Pull Request 20642: https://github.com/galaxyproject/galaxy/pull/20642
+.. _Pull Request 20788: https://github.com/galaxyproject/galaxy/pull/20788
+.. _Pull Request 20996: https://github.com/galaxyproject/galaxy/pull/20996
+.. _Pull Request 21003: https://github.com/galaxyproject/galaxy/pull/21003
+.. _Pull Request 20999: https://github.com/galaxyproject/galaxy/pull/20999
+.. _Pull Request 21006: https://github.com/galaxyproject/galaxy/pull/21006
+.. _Pull Request 21007: https://github.com/galaxyproject/galaxy/pull/21007
+.. _Pull Request 20985: https://github.com/galaxyproject/galaxy/pull/20985
+.. _Pull Request 21005: https://github.com/galaxyproject/galaxy/pull/21005
+.. _Pull Request 20754: https://github.com/galaxyproject/galaxy/pull/20754
+.. _Pull Request 21009: https://github.com/galaxyproject/galaxy/pull/21009
+.. _Pull Request 21012: https://github.com/galaxyproject/galaxy/pull/21012
+.. _Pull Request 21014: https://github.com/galaxyproject/galaxy/pull/21014
+.. _Pull Request 21017: https://github.com/galaxyproject/galaxy/pull/21017
+.. _Pull Request 21020: https://github.com/galaxyproject/galaxy/pull/21020
+.. _Pull Request 21018: https://github.com/galaxyproject/galaxy/pull/21018
+.. _Pull Request 21019: https://github.com/galaxyproject/galaxy/pull/21019
+.. _Pull Request 21022: https://github.com/galaxyproject/galaxy/pull/21022
+.. _Pull Request 21026: https://github.com/galaxyproject/galaxy/pull/21026
+.. _Pull Request 21045: https://github.com/galaxyproject/galaxy/pull/21045
+.. _Pull Request 20801: https://github.com/galaxyproject/galaxy/pull/20801
+.. _Pull Request 20757: https://github.com/galaxyproject/galaxy/pull/20757
+.. _Pull Request 20898: https://github.com/galaxyproject/galaxy/pull/20898
+.. _Pull Request 20987: https://github.com/galaxyproject/galaxy/pull/20987
+.. _Pull Request 21056: https://github.com/galaxyproject/galaxy/pull/21056
+.. _Pull Request 21055: https://github.com/galaxyproject/galaxy/pull/21055
+.. _Pull Request 21070: https://github.com/galaxyproject/galaxy/pull/21070
+.. _Pull Request 21081: https://github.com/galaxyproject/galaxy/pull/21081
+.. _Pull Request 21095: https://github.com/galaxyproject/galaxy/pull/21095
+.. _Pull Request 20821: https://github.com/galaxyproject/galaxy/pull/20821
+.. _Pull Request 21072: https://github.com/galaxyproject/galaxy/pull/21072
+.. _Pull Request 21094: https://github.com/galaxyproject/galaxy/pull/21094
+.. _Pull Request 21087: https://github.com/galaxyproject/galaxy/pull/21087
+.. _Pull Request 21091: https://github.com/galaxyproject/galaxy/pull/21091
+.. _Pull Request 21096: https://github.com/galaxyproject/galaxy/pull/21096
+.. _Pull Request 21035: https://github.com/galaxyproject/galaxy/pull/21035
+.. _Pull Request 21105: https://github.com/galaxyproject/galaxy/pull/21105
+.. _Pull Request 21112: https://github.com/galaxyproject/galaxy/pull/21112
+.. _Pull Request 21117: https://github.com/galaxyproject/galaxy/pull/21117
+.. _Pull Request 21115: https://github.com/galaxyproject/galaxy/pull/21115
+.. _Pull Request 21049: https://github.com/galaxyproject/galaxy/pull/21049
+.. _Pull Request 21060: https://github.com/galaxyproject/galaxy/pull/21060
+.. _Pull Request 21078: https://github.com/galaxyproject/galaxy/pull/21078
+.. _Pull Request 20424: https://github.com/galaxyproject/galaxy/pull/20424
+.. _Pull Request 21107: https://github.com/galaxyproject/galaxy/pull/21107
+.. _Pull Request 20427: https://github.com/galaxyproject/galaxy/pull/20427
+.. _Pull Request 20550: https://github.com/galaxyproject/galaxy/pull/20550
+.. _Pull Request 20558: https://github.com/galaxyproject/galaxy/pull/20558
+.. _Pull Request 20565: https://github.com/galaxyproject/galaxy/pull/20565
+.. _Pull Request 20585: https://github.com/galaxyproject/galaxy/pull/20585
+.. _Pull Request 20592: https://github.com/galaxyproject/galaxy/pull/20592
+.. _Pull Request 20609: https://github.com/galaxyproject/galaxy/pull/20609
+.. _Pull Request 20624: https://github.com/galaxyproject/galaxy/pull/20624
+.. _Pull Request 20666: https://github.com/galaxyproject/galaxy/pull/20666
+.. _Pull Request 20719: https://github.com/galaxyproject/galaxy/pull/20719
+.. _Pull Request 20737: https://github.com/galaxyproject/galaxy/pull/20737
+.. _Pull Request 20738: https://github.com/galaxyproject/galaxy/pull/20738
+.. _Pull Request 20744: https://github.com/galaxyproject/galaxy/pull/20744
+.. _Pull Request 20747: https://github.com/galaxyproject/galaxy/pull/20747
+.. _Pull Request 20776: https://github.com/galaxyproject/galaxy/pull/20776
+.. _Pull Request 20798: https://github.com/galaxyproject/galaxy/pull/20798
+.. _Pull Request 20805: https://github.com/galaxyproject/galaxy/pull/20805
+.. _Pull Request 20839: https://github.com/galaxyproject/galaxy/pull/20839
+.. _Pull Request 20868: https://github.com/galaxyproject/galaxy/pull/20868
+.. _Pull Request 20881: https://github.com/galaxyproject/galaxy/pull/20881
+.. _Pull Request 20912: https://github.com/galaxyproject/galaxy/pull/20912
+.. _Pull Request 20914: https://github.com/galaxyproject/galaxy/pull/20914
+.. _Pull Request 20943: https://github.com/galaxyproject/galaxy/pull/20943
+.. _Pull Request 20947: https://github.com/galaxyproject/galaxy/pull/20947
+.. _Pull Request 21025: https://github.com/galaxyproject/galaxy/pull/21025
+.. _Pull Request 19084: https://github.com/galaxyproject/galaxy/pull/19084
+.. _Pull Request 19225: https://github.com/galaxyproject/galaxy/pull/19225
+.. _Pull Request 19305: https://github.com/galaxyproject/galaxy/pull/19305
+.. _Pull Request 19318: https://github.com/galaxyproject/galaxy/pull/19318
+.. _Pull Request 19658: https://github.com/galaxyproject/galaxy/pull/19658
+.. _Pull Request 19973: https://github.com/galaxyproject/galaxy/pull/19973
+.. _Pull Request 20287: https://github.com/galaxyproject/galaxy/pull/20287
+.. _Pull Request 20288: https://github.com/galaxyproject/galaxy/pull/20288
+.. _Pull Request 20390: https://github.com/galaxyproject/galaxy/pull/20390
+.. _Pull Request 21051: https://github.com/galaxyproject/galaxy/pull/21051
+.. _Pull Request 21021: https://github.com/galaxyproject/galaxy/pull/21021
+.. _Pull Request 21130: https://github.com/galaxyproject/galaxy/pull/21130
+.. _Pull Request 21134: https://github.com/galaxyproject/galaxy/pull/21134
+.. _Pull Request 21138: https://github.com/galaxyproject/galaxy/pull/21138
+.. _Pull Request 20539: https://github.com/galaxyproject/galaxy/pull/20539
+.. _Pull Request 20629: https://github.com/galaxyproject/galaxy/pull/20629
+.. _Pull Request 21141: https://github.com/galaxyproject/galaxy/pull/21141
+.. _Pull Request 21145: https://github.com/galaxyproject/galaxy/pull/21145
+.. _Pull Request 21142: https://github.com/galaxyproject/galaxy/pull/21142
+.. _Pull Request 21140: https://github.com/galaxyproject/galaxy/pull/21140
+.. _Pull Request 21149: https://github.com/galaxyproject/galaxy/pull/21149
diff --git a/doc/source/releases/26.0_announce.rst b/doc/source/releases/26.0_announce.rst
new file mode 100644
index 00000000000..0628593ca82
--- /dev/null
+++ b/doc/source/releases/26.0_announce.rst
@@ -0,0 +1,6 @@
+
+:orphan:
+
+===========================================================
+26.0 Galaxy Release
+===========================================================
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 7832c65985d..2b6908c8b39 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   25.1_announce_user
    25.0_announce_user
    24.2_announce_user
    24.1_announce_user
diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index 789cf9acc0b..c8539c319ea 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -158,11 +158,17 @@ class DatasetCollectionManager:
                             substructure, allow_uninitialized_element=allow_uninitialized_element
                         )
 
+                # Preserve columns metadata from input structure for sample sheets
+                columns = None
+                if structure.columns_metadata and identifier in structure.columns_metadata:
+                    columns = structure.columns_metadata[identifier]
+
                 element = model.DatasetCollectionElement(
                     collection=dataset_collection,
                     element=element,
                     element_identifier=identifier,
                     element_index=index,
+                    columns=columns,
                 )
                 elements.append(element)
             dataset_collection.element_count = len(elements)
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3f6e6a55dae..03000433057 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -7378,7 +7378,11 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         minimize_copies=False,
         copy_hid=True,
     ):
-        new_collection = DatasetCollection(collection_type=self.collection_type, element_count=self.element_count)
+        new_collection = DatasetCollection(
+            collection_type=self.collection_type,
+            element_count=self.element_count,
+            column_definitions=self.column_definitions,
+        )
         for element in self.elements:
             element.copy_to_collection(
                 new_collection,
diff --git a/lib/galaxy/model/database_heartbeat.py b/lib/galaxy/model/database_heartbeat.py
index 84a84842db8..abffbf64625 100644
--- a/lib/galaxy/model/database_heartbeat.py
+++ b/lib/galaxy/model/database_heartbeat.py
@@ -96,9 +96,10 @@ class DatabaseHeartbeat:
             session.add(worker_process)
         # We only want a single process watching the various config files on the file system.
         # We just pick the max server name for simplicity
-        is_config_watcher = self.server_name == max(
+        webapp_servers = [
             p.server_name for p in self.get_active_processes(self.heartbeat_interval + 1) if p.app_type == WEBAPP
-        )
+        ]
+        is_config_watcher = bool(webapp_servers) and self.server_name == max(webapp_servers)
         if is_config_watcher != self.is_config_watcher:
             self.is_config_watcher = is_config_watcher
 
diff --git a/lib/galaxy/model/dataset_collections/structure.py b/lib/galaxy/model/dataset_collections/structure.py
index 3c0e53e1cc4..97d38319703 100644
--- a/lib/galaxy/model/dataset_collections/structure.py
+++ b/lib/galaxy/model/dataset_collections/structure.py
@@ -64,14 +64,17 @@ class UninitializedTree(BaseTree):
 class Tree(BaseTree):
     children_known = True
 
-    def __init__(self, children, collection_type_description, when_values=None):
+    def __init__(self, children, collection_type_description, when_values=None, columns_metadata=None):
         super().__init__(collection_type_description)
         self.children = children
         self.when_values = when_values
+        # columns_metadata is a dict mapping element_identifier to columns data
+        self.columns_metadata = columns_metadata or {}
 
     @staticmethod
     def for_dataset_collection(dataset_collection, collection_type_description):
         children = []
+        columns_metadata = {}
         for element in dataset_collection.elements:
             if collection_type_description.has_subcollections():
                 child_collection = element.child_collection
@@ -84,7 +87,10 @@ class Tree(BaseTree):
                 children.append((element.element_identifier, tree))
             else:
                 children.append((element.element_identifier, leaf))
-        return Tree(children, collection_type_description)
+            # Capture columns metadata from sample sheet collections
+            if element.columns is not None:
+                columns_metadata[element.element_identifier] = element.columns
+        return Tree(children, collection_type_description, columns_metadata=columns_metadata)
 
     def walk_collections(self, hdca_dict):
         return self._walk_collections(dict_map(lambda hdca: hdca.collection, hdca_dict))
@@ -142,11 +148,12 @@ class Tree(BaseTree):
         for identifier, structure in self.children:
             new_children.append((identifier, structure.multiply(other_structure)))
 
-        return Tree(new_children, new_collection_type)
+        # Preserve columns_metadata when multiplying
+        return Tree(new_children, new_collection_type, columns_metadata=self.columns_metadata.copy())
 
     def clone(self):
         cloned_children = [(_[0], _[1].clone()) for _ in self.children]
-        return Tree(cloned_children, self.collection_type_description)
+        return Tree(cloned_children, self.collection_type_description, columns_metadata=self.columns_metadata.copy())
 
     def __str__(self):
         return f"Tree[collection_type={self.collection_type_description},children=({','.join(f'{identifier_and_element[0]}={identifier_and_element[1]}' for identifier_and_element in self.children)})]"
diff --git a/lib/galaxy/model/migrations/dbrevisions.py b/lib/galaxy/model/migrations/dbrevisions.py
index 7585b2e59e7..23fcc838a83 100644
--- a/lib/galaxy/model/migrations/dbrevisions.py
+++ b/lib/galaxy/model/migrations/dbrevisions.py
@@ -14,5 +14,5 @@ REVISION_TAGS = {
     "24.1": "04288b6a5b25",
     "24.2": "a4c3ef999ab5",
     "25.0": "c716ee82337b",
-    "25.1": "cd26484899fb",
+    "25.1": "63dc6cca023f",
 }
diff --git a/lib/galaxy/tools/sample_sheet_to_tabular.xml b/lib/galaxy/tools/sample_sheet_to_tabular.xml
index a7a5f8fc100..d6be1f17d23 100644
--- a/lib/galaxy/tools/sample_sheet_to_tabular.xml
+++ b/lib/galaxy/tools/sample_sheet_to_tabular.xml
@@ -6,7 +6,13 @@
     <edam_operation>operation_3359</edam_operation>
   </edam_operations>
   <configfiles>
-    <configfile name="out_config"><![CDATA[#for $key in $input.keys()
+    <configfile name="out_config"><![CDATA[#if $include_headers and $input.collection.column_definitions
+#set $headers = [col_def['name'] for col_def in $input.collection.column_definitions]
+#set $header_string = '\t'.join($headers)
+#set $tab = '\t'
+element_identifier$tab$header_string
+#end if
+#for $key in $input.keys()
 #set $row = $input.sample_sheet_row($key)
 #set $row_as_string = '\t'.join(map(lambda x: str($none_replace) if x is None else (str($empty_replace) if x == "" else (str($bool_true_replace) if x is True else (str($bool_false_replace) if x is False else str(x)))), $row))
 #set $tab = '\t'
@@ -19,6 +25,8 @@ cp '$out_config' '$output'
 
   <inputs>
     <param type="data_collection" collection_type="sample_sheet,sample_sheet:paired,sample_sheet:paired_or_unpaired,sample_sheet:record" name="input" label="Sample sheet to convert" />
+    <param name="include_headers" label="Include column headers" type="boolean" checked="false" help="If enabled, the first line of output will contain the column names from the sample sheet definition.">
+    </param>
     <param name="none_replace" label="Replace 'null' values with" type="text" value="" help="Default is just an empty string '', but in some cases '-' might read better.">
     </param>
     <param name="empty_replace" label="Replace empty string values with" type="text" value="" help="Default is just to keep the empty string '', but in some cases '-' might read better.">
@@ -39,5 +47,11 @@ Synopsis
 
 Takes a sample sheet dataset collection and converts the sample sheet metadata into a tabular dataset.
 
+The output is a tab-separated file where each row corresponds to an element in the sample sheet collection.
+The first column contains the element identifier, followed by columns for each metadata field defined in the sample sheet.
+
+When "Include column headers" is enabled, the first row will contain the column names, with "element_identifier"
+as the first column followed by the names from the sample sheet column definitions.
+
   ]]></help>
 </tool>
diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index 36792896a49..6d4bd6d1eb0 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -224,6 +224,12 @@ class WorkflowInvoker:
         remaining_steps = self.progress.remaining_steps()
         delayed_steps = False
         max_jobs_per_iteration_reached = False
+
+        # Pre-populate outputs for all input steps so subworkflows can access them
+        for step in self.workflow_invocation.workflow.steps:
+            if step.is_input_type:
+                self.progress._ensure_input_step_outputs_populated(step)
+
         for step, workflow_invocation_step in remaining_steps:
             max_jobs_to_schedule = self.progress.maximum_jobs_to_schedule_or_none
             if max_jobs_to_schedule is not None and max_jobs_to_schedule <= 0:
@@ -255,13 +261,29 @@ class WorkflowInvoker:
                 self.progress.mark_step_outputs_delayed(step, why=de.why)
             except Exception as e:
                 log_function = log.error
-                if isinstance(e, modules.FailWorkflowEvaluation) and e.why.reason in FAILURE_REASONS_EXPECTED:
-                    log_function = log.info
+                failure_details = []
+                if isinstance(e, modules.FailWorkflowEvaluation):
+                    if e.why.reason in FAILURE_REASONS_EXPECTED:
+                        log_function = log.info
+                    failure_details.append(f"reason={e.why.reason}")
+                    if hasattr(e.why, "output_name") and e.why.output_name:
+                        failure_details.append(f"output_name={e.why.output_name}")
+                    if hasattr(e.why, "dependent_workflow_step_id") and e.why.dependent_workflow_step_id:
+                        failure_details.append(f"dependent_step_id={e.why.dependent_workflow_step_id}")
+                    if hasattr(e.why, "workflow_step_id") and e.why.workflow_step_id:
+                        failure_details.append(f"failed_step_id={e.why.workflow_step_id}")
+                    if hasattr(e.why, "details") and e.why.details:
+                        failure_details.append(f"details={e.why.details}")
+                else:
+                    failure_details.append(f"{type(e).__name__}: {str(e)}")
+                failure_reason = ", ".join(failure_details) if failure_details else "unknown"
+
                 log_function(
-                    "Failed to schedule %s for %s, problem occurred on %s.",
+                    "Failed to schedule %s for %s, problem occurred on %s. Failure reason: %s",
                     self.workflow_invocation.log_str(),
                     self.workflow_invocation.workflow.log_str(),
                     step.log_str(),
+                    failure_reason,
                 )
                 if isinstance(e, MessageException):
                     # This is the highest level at which we can inject the step id
@@ -578,14 +600,26 @@ class WorkflowProgress:
         if outputs is None:
             outputs = {}
 
-        if self.inputs_by_step_id:
-            step_id = step.id
-            if step_id not in self.inputs_by_step_id and "output" not in outputs:
-                default_value = step.get_input_default_value(NO_REPLACEMENT)
-                outputs["output"] = default_value
-            elif step_id in self.inputs_by_step_id:
-                if self.inputs_by_step_id[step_id] is not None or "output" not in outputs:
+        # Check if we have a pre-populated value from _ensure_input_step_outputs_populated
+        # This takes precedence over values from step.state.inputs for input steps
+        # Only use pre-populated values when inputs_by_step_id was available during pre-population
+        if step.is_input_type and self.inputs_by_step_id and step.id in self.outputs:
+            pre_populated = self.outputs.get(step.id)
+            if isinstance(pre_populated, dict) and "output" in pre_populated:
+                outputs["output"] = pre_populated["output"]
+
+        # Output not yet set
+        if "output" not in outputs:
+            if self.inputs_by_step_id:
+                step_id = step.id
+                if step_id not in self.inputs_by_step_id:
+                    default_value = step.get_input_default_value(NO_REPLACEMENT)
+                    outputs["output"] = default_value
+                elif self.inputs_by_step_id[step_id] is not None or "output" not in outputs:
                     outputs["output"] = self.inputs_by_step_id[step_id]
+            else:
+                # When inputs_by_step_id is None (e.g., during recovery), use default
+                outputs["output"] = step.get_input_default_value(NO_REPLACEMENT)
 
         if step.label and step.type == "parameter_input" and "output" in outputs:
             self.runtime_replacements[step.label] = str(outputs["output"])
@@ -651,6 +685,32 @@ class WorkflowProgress:
             raise MessageException(f"Failed to find persisted subworkflow invocation for step [{step.order_index + 1}]")
         return subworkflow_invocation
 
+    def _ensure_input_step_outputs_populated(self, step: "WorkflowStep") -> None:
+        """Pre-populate outputs for input steps that haven't executed yet.
+
+        Input steps have no dependencies, so their output value can be determined
+        immediately. This allows subworkflows to access parent input values before
+        the input step formally executes.
+        """
+        if not step.is_input_type or step.id in self.outputs:
+            return
+
+        # Check if step already executed - if so, skip pre-population
+        step_invocations = self.workflow_invocation.step_invocations_by_step_id()
+        if step.id in step_invocations:
+            invocation_step = step_invocations[step.id]
+            if invocation_step.state == "scheduled":
+                return
+
+        # Determine output value from inputs_by_step_id or default
+        outputs = {}
+        if step.id not in self.inputs_by_step_id:
+            outputs["output"] = step.get_input_default_value(NO_REPLACEMENT)
+        else:
+            outputs["output"] = self.inputs_by_step_id[step.id]
+
+        self.outputs[step.id] = outputs
+
     def subworkflow_invoker(
         self,
         trans: "WorkRequestContext",
diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py
index 4c5ae2773b6..c2e0797784c 100644
--- a/lib/galaxy_test/api/test_dataset_collections.py
+++ b/lib/galaxy_test/api/test_dataset_collections.py
@@ -16,6 +16,7 @@ from galaxy_test.base.decorators import requires_new_user
 from galaxy_test.base.populators import (
     DatasetCollectionPopulator,
     DatasetPopulator,
+    skip_without_tool,
 )
 from ._framework import ApiTestCase
 
@@ -427,6 +428,86 @@ class TestDatasetCollectionsApi(ApiTestCase):
         assert row_1[0] == 45
         # TODO: test case where column definition does not match supplied data
 
+    @skip_without_tool("cat1")
+    def test_sample_sheet_map_over_preserves_columns(self, history_id):
+        """Test that mapping cat1 over a sample sheet preserves columns metadata."""
+        # Create a sample sheet collection with columns metadata
+        contents = [
+            ("sample1", "content1"),
+            ("sample2", "content2"),
+            ("sample3", "content3"),
+        ]
+        sample_sheet_identifiers = self.dataset_collection_populator.list_identifiers(history_id, contents)
+        payload = dict(
+            name="test sample sheet",
+            instance_type="history",
+            history_id=history_id,
+            element_identifiers=sample_sheet_identifiers,
+            collection_type="sample_sheet",
+            column_definitions=[
+                {"type": "int", "name": "replicate", "optional": False},
+                {"type": "string", "name": "condition", "optional": False},
+            ],
+            rows={
+                "sample1": [1, "control"],
+                "sample2": [2, "treatment"],
+                "sample3": [3, "control"],
+            },
+        )
+        create_response = self._post("dataset_collections", payload, json=True)
+        sample_sheet = self._check_create_response(create_response)
+        hdca_id = sample_sheet["id"]
+
+        # Verify the input sample sheet has columns metadata
+        input_elements = sample_sheet["elements"]
+        assert len(input_elements) == 3
+        assert input_elements[0]["columns"] == [1, "control"]
+        assert input_elements[1]["columns"] == [2, "treatment"]
+        assert input_elements[2]["columns"] == [3, "control"]
+
+        # Run cat1 on the sample sheet collection in batch mode (mapping over it)
+        inputs = {
+            "input1": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]},
+        }
+        run = self.dataset_populator.run_tool("cat1", inputs=inputs, history_id=history_id)
+        self.dataset_populator.wait_for_history_jobs(history_id)
+
+        # Get the implicit output collection
+        implicit_collections = run["implicit_collections"]
+        assert len(implicit_collections) == 1, f"Expected 1 implicit collection, got {len(implicit_collections)}"
+        output_collection = implicit_collections[0]
+
+        # Fetch the full collection details including elements
+        collection_details = self.dataset_populator.get_history_collection_details(
+            history_id, content_id=output_collection["id"]
+        )
+
+        # Verify that the output collection preserved the columns metadata
+        output_elements = collection_details["elements"]
+        assert len(output_elements) == 3, f"Expected 3 output elements, got {len(output_elements)}"
+
+        # Check that columns metadata was preserved for each element
+        self._assert_has_keys(output_elements[0], "columns")
+        assert output_elements[0]["columns"] == [
+            1,
+            "control",
+        ], f"Expected [1, 'control'], got {output_elements[0]['columns']}"
+        assert output_elements[0]["element_identifier"] == "sample1"
+
+        self._assert_has_keys(output_elements[1], "columns")
+        assert output_elements[1]["columns"] == [
+            2,
+            "treatment",
+        ], f"Expected [2, 'treatment'], got {output_elements[1]['columns']}"
+        assert output_elements[1]["element_identifier"] == "sample2"
+
+        self._assert_has_keys(output_elements[2], "columns")
+        assert output_elements[2]["columns"] == [
+            3,
+            "control",
+        ], f"Expected [3, 'control'], got {output_elements[2]['columns']}"
+        assert output_elements[2]["element_identifier"] == "sample3"
+
     def test_workbook_download(self):
         xlsx_file = self.dataset_collection_populator.download_workbook(
             "sample_sheet",
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index fd93c0ca606..447cf454819 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -5528,6 +5528,100 @@ test_data:
                 assert_ok=True,
             )
 
+    def test_run_subworkflow_with_optional_parent_input_connected_but_not_provided(self):
+        """Test subworkflow when parent's optional input is connected but not provided.
+
+        This test verifies the fix for a bug where:
+        1. Parent workflow has an OPTIONAL input
+        2. That optional input IS CONNECTED to the subworkflow's input
+        3. But NO DATA is provided for the parent's optional input
+        4. Subworkflow has DELAYED SCHEDULING (via $link)
+
+        After the fix, the parent's optional input outputs are pre-populated with NO_REPLACEMENT
+        before the subworkflow executes, allowing it to properly handle the missing value.
+
+        This is different from the case where subworkflow inputs are completely
+        unconnected, which was fixed in 2022.
+        """
+        with self.dataset_populator.test_history() as history_id:
+            # Workflow with OPTIONAL input that IS CONNECTED to subworkflow
+            # input data is not provided
+            workflow = """
+class: GalaxyWorkflow
+inputs:
+  parent_required:
+    type: data
+  parent_optional:
+    type: data
+    optional: true
+steps:
+  nested_workflow:
+    in:
+      required_input: parent_required
+      optional_input: parent_optional
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        required_input: data
+        optional_input:
+          type: data
+          optional: true
+      steps:
+        expression:
+          tool_id: expression_parse_int
+          state:
+            input1: 1
+        head:
+          tool_id: head
+          in:
+            input: required_input
+          state:
+            lineNum:
+              $link: expression/out1
+        count_multi_file:
+          tool_id: count_multi_file
+          in:
+            input1:
+            - optional_input
+            - head/out_file1
+test_data:
+  parent_required:
+    value: 1.bed
+    type: File
+"""
+
+            # After the fix, this should now succeed
+            summary = self._run_workflow(
+                workflow,
+                history_id=history_id,
+                wait=True,
+                assert_ok=True,
+            )
+
+            # Check parent invocation
+            parent_invocation = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)
+
+            # Get the subworkflow invocation
+            subworkflow_step = None
+            for step in parent_invocation["steps"]:
+                if step.get("subworkflow_invocation_id"):
+                    subworkflow_step = step
+                    break
+
+            assert subworkflow_step is not None, "No subworkflow step found"
+
+            subworkflow_invocation_id = subworkflow_step["subworkflow_invocation_id"]
+            subworkflow_invocation = self.workflow_populator.get_invocation(subworkflow_invocation_id)
+
+            # The subworkflow should have succeeded
+            assert (
+                subworkflow_invocation["state"] == "scheduled"
+            ), f"Expected subworkflow to succeed, got state: {subworkflow_invocation['state']}"
+
+            # Should not have error messages
+            messages = subworkflow_invocation.get("messages", [])
+            assert len(messages) == 0, f"Expected no error messages, got: {messages}"
+
     def test_run_with_non_optional_data_unspecified_fails_invocation(self):
         with self.dataset_populator.test_history() as history_id:
             error = self._run_jobs(
diff --git a/test/unit/data/dataset_collections/test_matching.py b/test/unit/data/dataset_collections/test_matching.py
index 60de9c300ef..50cb6af35d4 100644
--- a/test/unit/data/dataset_collections/test_matching.py
+++ b/test/unit/data/dataset_collections/test_matching.py
@@ -254,6 +254,7 @@ class MockCollectionElement:
         self.element_identifier = element_identifier
         self.child_collection = collection
         self.hda = None
+        self.columns = None
 
 
 class MockHDAElement:
@@ -261,6 +262,7 @@ class MockHDAElement:
         self.element_identifier = element_identifier
         self.child_collection = False
         self.hda = object()
+        self.columns = None
 
 
 collection_instance = MockCollectionInstance