Move custom schema documentation to pipeline-schema overview

netlify.toml

@@ -21,6 +21,9 @@
   EXCLUDE_PLATFORM_API="true"
   EXCLUDE_PLATFORM_OPENAPI="true"
 
+# Seqera API docs are too large to host / build on netlify on their own.
+# The appropriate ENVVAR is set to disable the API Builds on Netlify for the main docs site.
+
 # Asset and image routing handled by Edge Function
 # See .netlify/edge-functions/asset-proxy.js
 [[edge_functions]]

platform-cloud/docs/pipeline-schema/overview.md

@@ -11,6 +11,37 @@ You can populate the parameters in the pipeline by uploading a YAML or JSON file
 
 See [nf-core/rnaseq](https://github.com/nf-core/rnaseq/blob/e049f51f0214b2aef7624b9dd496a404a7c34d14/nextflow_schema.json) as an example of the pipeline parameters that can be represented by a JSON schema file.
 
+### Define pipeline schema
+
+When adding or editing a pipeline, you can select one of three schema options to control parameter validation and the launch form:
+
+1. **Repository default**: Use the default schema provided by the Pipeline git repository.
+2. **Repository path**: Use a schema at a specific path in the repository.
+3. **Seqera Platform schema**: Use a Nextflow JSON schema stored in Seqera Platform (overrides repository).
+
+The selected schema controls which pipeline parameters are exposed in the launch form. This allows you to restrict the parameters visible to launch users, simplifying the launch experience and preventing modification of parameters that should remain fixed.
+
+#### Seqera Platform schema
+
+Users with [Maintain or higher](../orgs-and-teams/roles.md) permissions can upload a custom `nextflow_schema.json` file directly to Seqera Platform. When you upload a Platform schema:
+
+- The schema content is validated to ensure it's a valid JSON schema.
+- The Platform schema controls which parameters appear in the pipeline launch form.
+- Changes to the Platform schema trigger a new draft version of the pipeline.
+- The Platform schema is applied to all launches using that pipeline version.
+
+To add or update a Seqera Platform schema:
+
+1. Navigate to **Add pipeline** or select **Edit** for an existing pipeline.
+2. Select **Seqera Platform schema** from the schema options.
+3. In the **Seqera Platform schema** field, paste your custom Nextflow schema JSON.
+4. The schema is validated automatically as you enter it.
+5. Select **Add** or **Save** to create a new draft version with the Platform schema.
+
+:::note
+The schema `id` field must be unique. If you're pasting pipeline schema contents from an existing pipeline schema file, update the `id` field to a unique value, or remove it.
+:::
+
 ### Building pipeline schema files
 
 The pipeline schema is based on [json-schema.org](https://json-schema.org/) syntax, with some additional conventions. While you can create your pipeline schema manually, we highly recommend using [nf-core tools](https://nf-co.re/tools/#pipeline-schema), a toolset for developing Nextflow pipelines built by the nf-core community.

platform-cloud/docs/pipelines/versioning.md

@@ -42,7 +42,8 @@ New draft versions are automatically generated when you modify the following:
   - **Image**
   - **Description**
   - **Labels**
-- Custom Nextflow schema file (see [Custom schema](#custom-schema))
+  - **Resource labels**
+- Pipeline schema selection (see [Define pipeline schema](../pipeline-schema/overview.md#define-pipeline-schema))
 
 Published versions provide a stable reference for team-wide pipeline launches. Users with Maintain or higher permissions can publish a draft version, giving it a name and optionally setting it as the default version. This makes important configurations easy to identify, share, and promote across your team.
 
@@ -52,23 +53,11 @@ A pipeline's default version is shown in the Launchpad and automatically selecte
 
 Seqera maintains a history of all draft and published versions, providing an audit trail of pipeline evolution.
 
-#### Custom schema
+#### Seqera Platform schema
 
-Users with Maintain or higher permissions can upload a custom `nextflow_schema.json` file to control which pipeline parameters are exposed in the launch form. This allows you to restrict the parameters visible to launch users, simplifying the launch experience and preventing modification of parameters that should remain fixed.
+Users with Maintain or higher permissions can upload a `nextflow_schema.json` file to Seqera Platform to control which pipeline parameters appear in the launch form. Changes to the Seqera Platform schema trigger a new draft version of the pipeline.
 
-The custom schema field is available when adding or editing a pipeline. When you upload a custom schema:
-
-- The schema content is validated to ensure it's a valid Nextflow schema
-- The custom schema controls which parameters appear in the pipeline launch form
-- Changes to the custom schema trigger a new draft version of the pipeline
-- The custom schema is applied to all launches using that pipeline version
-
-To add or update a custom schema:
-
-1. Navigate to **Add pipeline** or select **Edit** for an existing pipeline
-2. In the **Custom Schema JSON** field, paste your custom Nextflow schema JSON
-3. The schema is validated automatically as you enter it
-4. Select **Add** or **Save** to create a new draft version with the custom schema
+For more information, see [Define pipeline schema](../pipeline-schema/overview.md#define-pipeline-schema).
 
 #### Manage pipeline versions
 

platform-enterprise_docs/pipelines/versioning.md

@@ -26,6 +26,7 @@ New draft versions are automatically generated during pipeline edit or launch wh
   - **Image**
   - **Description**
   - **Labels**
+  - **Resource labels**
 
 Published versions provide a stable reference for team-wide pipeline launches. Users with Maintain or higher permissions can publish a draft version, giving it a name and optionally setting it as the default version. This makes important configurations easy to identify, share, and promote across your team.
 

platform-enterprise_versioned_docs/version-25.3/pipeline-schema/overview.md

@@ -11,6 +11,37 @@ You can populate the parameters in the pipeline by uploading a YAML or JSON file
 
 See [nf-core/rnaseq](https://github.com/nf-core/rnaseq/blob/e049f51f0214b2aef7624b9dd496a404a7c34d14/nextflow_schema.json) as an example of the pipeline parameters that can be represented by a JSON schema file.
 
+### Define pipeline schema
+
+When adding or editing a pipeline, you can select one of three schema options to control parameter validation and the launch form:
+
+1. **Repository default**: Use the default schema provided by the Pipeline git repository.
+2. **Repository path**: Use a schema at a specific path in the repository.
+3. **Seqera Platform schema**: Use a Nextflow JSON schema stored in Seqera Platform (overrides repository).
+
+The selected schema controls which pipeline parameters are exposed in the launch form. This allows you to restrict the parameters visible to launch users, simplifying the launch experience and preventing modification of parameters that should remain fixed.
+
+#### Seqera Platform schema
+
+Users with [Maintain or higher](../orgs-and-teams/roles.md) permissions can upload a custom `nextflow_schema.json` file directly to Seqera Platform. When you upload a Platform schema:
+
+- The schema content is validated to ensure it's a valid JSON schema.
+- The Platform schema controls which parameters appear in the pipeline launch form.
+- Changes to the Platform schema trigger a new draft version of the pipeline.
+- The Platform schema is applied to all launches using that pipeline version.
+
+To add or update a Seqera Platform schema:
+
+1. Navigate to **Add pipeline** or select **Edit** for an existing pipeline.
+2. Select **Seqera Platform schema** from the schema options.
+3. In the **Seqera Platform schema** field, paste your custom Nextflow schema JSON.
+4. The schema is validated automatically as you enter it.
+5. Select **Add** or **Save** to create a new draft version with the Platform schema.
+
+:::note
+The schema `id` field must be unique. If you're pasting pipeline schema contents from an existing pipeline schema file, update the `id` field to a unique value, or remove it.
+:::
+
 ### Building pipeline schema files
 
 The pipeline schema is based on [json-schema.org](https://json-schema.org/) syntax, with some additional conventions. While you can create your pipeline schema manually, we highly recommend using [nf-core tools](https://nf-co.re/tools/#pipeline-schema), a toolset for developing Nextflow pipelines built by the nf-core community.

platform-enterprise_versioned_docs/version-25.3/pipelines/versioning.md

@@ -7,8 +7,6 @@ tags: [pipelines, versioning, nextflow, parameters]
 
 Seqera's pipeline versioning system captures configuration changes as new draft versions of the pipeline, ensuring configuration traceability and execution reproducibility. Users with [Maintain or higher](../orgs-and-teams/roles.md) permissions can edit and publish draft versions, creating published versions that teams can reference and launch consistently.
 
-To ensure fully reproducible behavior for pipelines configured with a branch or tag revision, it is essential to pin the commit ID of the workflow repository. This is because the 'HEAD' state of the repository can change over time. For more details see [Git revision management](https://docs.seqera.io/platform-enterprise/pipelines/revision).
-
 :::tip
 For deterministic and reproducible pipeline execution, use [commit ID pinning](revision.md) for published pipeline versions. This ensures the same workflow code is used across all launches of that version.
 :::
@@ -45,7 +43,8 @@ New draft versions are automatically generated during pipeline edit or launch wh
   - **Image**
   - **Description**
   - **Labels**
-- Custom Nextflow schema file (see [Custom schema](#custom-schema))
+  - **Resource labels**
+- Pipeline schema selection (see [Define pipeline schema](../pipeline-schema/overview.md#define-pipeline-schema))
 
 Published versions provide a stable reference for team-wide pipeline launches. Users with Maintain or higher permissions can publish a draft version, giving it a name and optionally setting it as the default version. This makes important configurations easy to identify, share, and promote across your team.
 
@@ -55,23 +54,11 @@ A pipeline's default version is shown in the Launchpad and automatically selecte
 
 Seqera maintains a history of all draft and published versions, providing an audit trail of pipeline evolution.
 
-#### Custom schema
-
-Users with [Maintain or higher](../orgs-and-teams/roles.md) permissions can upload a custom `nextflow_schema.json` file to control which pipeline parameters are exposed in the launch form. This allows you to restrict the parameters visible to launch users, simplifying the launch experience and preventing modification of parameters that should remain fixed.
-
-The custom schema field is available when adding or editing a pipeline. When you upload a custom schema:
-
-- The schema content is validated to ensure it's a valid Nextflow schema
-- The custom schema controls which parameters appear in the pipeline launch form
-- Changes to the custom schema trigger a new draft version of the pipeline
-- The custom schema is applied to all launches using that pipeline version
+#### Seqera Platform schema
 
-To add or update a custom schema:
+Users with [Maintain or higher](../orgs-and-teams/roles.md) permissions can upload a `nextflow_schema.json` file to Seqera Platform to control which pipeline parameters appear in the launch form. Changes to the Seqera Platform schema trigger a new draft version of the pipeline.
 
-1. Navigate to **Add pipeline** or select **Edit** for an existing pipeline
-2. In the **Custom Schema JSON** field, paste your custom Nextflow schema JSON
-3. The schema is validated automatically as you enter it
-4. Select **Add** or **Save** to create a new draft version with the custom schema
+For more information, see [Define pipeline schema](../pipeline-schema/overview.md#define-pipeline-schema).
 
 ### Manage pipeline versions