feature(datasets): Add linked datasets

platform-cloud/docs/data/datasets.md

@@ -2,25 +2,30 @@
 title: "Datasets"
 description: "Using datasets in Seqera Platform."
 date created: "2023-04-23"
-last updated: "2025-10-06"
+last updated: "2026-03-27"
 tags: [datasets]
 ---
 
-:::note
-This feature is only available in organization workspaces.
-:::
-
-Datasets in Seqera are CSV (comma-separated values) and TSV (tab-separated values) files stored in a workspace. They are used as inputs to pipelines to simplify data management, minimize user data-input errors, and facilitate reproducible workflows.
+Datasets are CSV (comma-separated values) and TSV (tab-separated values) files stored in, or linked to, a workspace. They are used as inputs to pipelines to simplify data management, minimize user data-input errors, and facilitate reproducible workflows.
 
 On the datasets screen, you can:
 
+- Upload directly or link to an externally hosted dataset.
 - View the count of pipeline runs in the workspace that have used a specific dataset input.
 - Apply multiple labels to datasets for easier searching and grouping.
 - Sort datasets by name, most recently updated, and most recently used.
 - Hide datasets that are not used in the workspace.
 - View dataset metadata (created by, last updated, last used).
 - Edit dataset details (name, description, and labels).
-- Upload new versions of a dataset.
+- Create new versions of a uploaded dataset.
+
+## Benefits
+
+- Datasets reduce errors that occur due to manual data entry when you launch pipelines.
+- Datasets can be generated automatically in response to events (such as S3 storage new file notifications).
+- Datasets can streamline differential data analysis when using the same pipeline to launch a run for each dataset as it becomes available.
+
+## Format
 
 The most commonly used datasets for Nextflow pipelines are samplesheets, where each row consists of a sample, the location of files for that sample (such as FASTQ files), and other sample details. For example, [*nf-core/rnaseq*](https://github.com/nf-core/rnaseq) works with input datasets (samplesheets) containing sample names, FASTQ file locations, and indications of strandedness. The Seqera Community Showcase sample dataset for *nf-core/rnaseq* looks like this:
 
@@ -40,39 +45,60 @@ The most commonly used datasets for Nextflow pipelines are samplesheets, where e
 Use [Data Explorer](../data/data-explorer) to browse for cloud storage objects directly and copy the object paths to be used in your datasets.
 :::
 
-The combination of datasets, [secrets](../secrets/overview), and [actions](../pipeline-actions/overview) allows you to automate workflows to curate your data and maintain and launch pipelines based on specific events. See [here](https://seqera.io/blog/workflow-automation/) for an example of pipeline workflow automation using Seqera.
+### Automation and pipeline schemas
 
-- Datasets reduce errors that occur due to manual data entry when you launch pipelines.
-- Datasets can be generated automatically in response to events (such as S3 storage new file notifications).
-- Datasets can streamline differential data analysis when using the same pipeline to launch a run for each dataset as it becomes available.
+The combination of datasets, [secrets](../secrets/overview), and [actions](../pipeline-actions/overview) allows you to automate workflows to curate your data and maintain and launch pipelines based on specific events. See [workflow-automation](https://seqera.io/blog/workflow-automation/) for an example of pipeline workflow automation.
 
 For your pipeline to use your dataset as input during runtime, information about the dataset and file format must be included in the relevant parameters of your [pipeline schema](../pipeline-schema/overview). The pipeline schema specifies the accepted dataset file type in the `mimetype` attribute (either `text/csv` or `text/tsv`).
 
-## Dataset validation and file content requirements
+## Dataset file content requirements and validation
+
+Datasets can point to files stored in various locations, such as Amazon S3, GitHub, or Hugging Face. To stage the file paths defined in the dataset, Nextflow requires access to the infrastructure where the files reside, whether on cloud or HPC systems. Add the access keys for data sources that require authentication to your [secrets](../secrets/overview).
 
+
+:::note
 Seqera doesn't validate your dataset file contents. While datasets can contain static file links, you're responsible for maintaining the access to that data.
+:::
 
-Datasets can point to files stored in various locations, such as Amazon S3 or GitHub. To stage the file paths defined in the dataset, Nextflow requires access to the infrastructure where the files reside, whether on cloud or HPC systems. Add the access keys for data sources that require authentication to your [secrets](../secrets/overview).
+## Adding a dataset
 
-## Create a dataset
+All Seqera user roles have access to the datasets feature in organization workspaces. There are two ways to add a dataset:
 
-All Seqera user roles have access to the datasets feature in organization workspaces. 
+1. Direct upload: This is the best option if immutability is a requirement but size cannot exceed 10 MB.
+1. Link to an externally hosted file: This is the best option for very large size files but relies on the external hosting service for availability and immutability.
 
-:::note
-The size of the dataset file cannot exceed 10 MB.
+### Direct upload
+
+1. In the sidebar navigation, select **Datasets**.
+1. Select **Add Dataset** and choose **Upload file**.
+1. Complete the **Name** and **Description** fields using information relevant to your dataset.
+1. Optionally add one or more **Labels** to your dataset. You can use labels as a search filter but they don't apply to other resources in Seqera.
+1. Upload a dataset to your workspace with drag-and-drop or use the **Upload file** file explorer dialog.
+1. For datasets that use their first row for column names, customize the dataset view using the **Set first row as header** option.
+1. Select **Add**.
+
+:::warning
+The size of the uploaded dataset file cannot exceed 10 MB.
 :::
 
-1. In the sidebar navigation, select the **Datasets** link under the Data heading in your organization workspace.
-2. Select **Add Dataset**.
-3. Complete the **Name** and **Description** fields using information relevant to your dataset.
-4. Optionally add one or more **Labels** to your dataset. You can use labels as a search filter but they don't apply to other resources in Seqera.
-4. Upload a dataset to your workspace with drag-and-drop or use the system "Upload file" file explorer dialog.
-5. For datasets that use their first row for column names, customize the dataset view using the **Set first row as header** option.
-6. Select **Add**. 
+### Link to an externally hosted file
+
+1. In the sidebar navigation, select **Datasets**.
+1. Select **Add Dataset** and choose **Link to URL**.
+1. Complete the **Name** and **Description** fields using information relevant to your dataset.
+1. Optionally add one or more **Labels** to your dataset. You can use labels as a search filter but they don't apply to other resources in Seqera.
+1. Copy and paste the dataset URL into the **Dataset URL** field
+1. For datasets that use their first row for column names, customize the dataset view using the **Set first row as header** option.
+1. Select **Add**.
+1. The dataset will be displayed with a `Linked` badge for easy identification.
 
 ## Manage dataset versions
 
-Seqera can manage multiple versions of an existing dataset.
+For directly uploaded datasets, Seqera can manage multiple versions.
+
+:::note
+For linked datasets, versioning is unavailable.
+:::
 
 ### Adding a dataset version
 
@@ -105,7 +131,8 @@ For compliance reasons, datasets or dataset versions cannot be deleted, they can
 
 Once disabled, a dataset version cannot be re-enabled.
 :::
-### Use a dataset
+
+## Using a dataset
 
 To use a dataset with pipelines added to your workspace:
 
@@ -117,7 +144,7 @@ To use a dataset with pipelines added to your workspace:
 The input field drop-down menu will only display datasets that match the file type specified in the `nextflow_schema.json` of the chosen pipeline. If the schema specifies `"mimetype": "text/csv"`, no TSV datasets will be available for use with that pipeline, and vice-versa. If multiple dataset versions exist, the pipeline input will always default to the **latest** version.
 :::
 
-## Manage datasets
+## Managing datasets
 
 **View runs**
 
@@ -135,11 +162,11 @@ You can toggle between **Visible**, **Hidden**, and **All** datasets in the **Sh
 :::note
 Hidden datasets do not count toward your per workspace quota.
 :::
+
 **Filter datasets**
 
 Filter the list of datasets to only display datasets that match one or more filters defined in the **Search datasets** field. Select the info icon to see the list of available filters.
 
 **Edit dataset details**
 
 Select the three dots next to a dataset to edit the name, description, and labels associated with a dataset.
-

platform-cloud/docs/troubleshooting_and_faqs/studios_troubleshooting.md

@@ -2,7 +2,7 @@
 title: "Studios"
 description: "Studios troubleshooting with Seqera Platform."
 date created: "2024-08-26"
-last updated: "2025-08-08"
+last updated: "2026-03-27"
 tags: [faq, help, studios, troubleshooting]
 ---
 
@@ -93,6 +93,10 @@ Setting the environment variable _inside_ an already running Studio session by e
 This is an experimental feature and may cause consistency issues in the Fusion namespace, resulting in data loss.
 :::
 
+## When starting an existing Studio session, extra processes are not automatically restarted
+
+Any process that is manually started in a running Studio session (e.g. `eval $(ssh-agent)`) will not be automatically restarted on a Studio restart. This is because any user initiated daemon process is not managed by the Connect client and therefore the Studio session does not manage it. To add extra processes that are automatically started at each Studio restart would require a user-defined startup script or an integrated supervisor (e.g. `s6`, `s6-overlay`, `supervisord`), both of which are currently unsupported.
+
 ## Container template image security scan false positives
 
 ### VS Code

platform-enterprise_docs/troubleshooting_and_faqs/studios_troubleshooting.md

@@ -93,6 +93,10 @@ Setting the environment variable _inside_ an already running Studio session by e
 This is an experimental feature and may cause consistency issues in the Fusion namespace, resulting in data loss.
 :::
 
+## When starting an existing Studio session, extra processes are not automatically restarted
+
+Any process that is manually started in a running Studio session (e.g. `eval $(ssh-agent)`) will not be automatically restarted on a Studio restart. This is because any user initiated daemon process is not managed by the Connect client and therefore the Studio session does not manage it. To add extra processes that are automatically started at each Studio restart would require a user-defined startup script or an integrated supervisor (e.g. `s6`, `s6-overlay`, `supervisord`), both of which are currently unsupported.
+
 ## Container template image security scan false positives
 
 ### VS Code

platform-enterprise_versioned_docs/version-25.3/troubleshooting_and_faqs/studios_troubleshooting.md

@@ -93,6 +93,10 @@ Setting the environment variable _inside_ an already running Studio session by e
 This is an experimental feature and may cause consistency issues in the Fusion namespace, resulting in data loss.
 :::
 
+## When starting an existing Studio session, extra processes are not automatically restarted
+
+Any process that is manually started in a running Studio session (e.g. `eval $(ssh-agent)`) will not be automatically restarted on a Studio restart. This is because any user initiated daemon process is not managed by the Connect client and therefore the Studio session does not manage it. To add extra processes that are automatically started at each Studio restart would require a user-defined startup script or an integrated supervisor (e.g. `s6`, `s6-overlay`, `supervisord`), both of which are currently unsupported.
+
 ## Container template image security scan false positives
 
 ### VS Code