docs: Add note and troubleshooting for nested config

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

@@ -51,6 +51,12 @@ When you run the `nf-core schema build` command in your pipeline root directory,
 The nf-core community creates the schema builder but it can be used with any Nextflow pipeline.
 :::
 
+:::note Null and blank parameter values
+When you launch a pipeline, the launch form validates your parameters against the pipeline schema and blocks the launch if validation fails. Seqera Platform removes top-level parameters with `null` or blank values before validation. This handling doesn't apply to parameters nested inside object-typed groups, such as `params.alignment.reference`. The launch form validates nested parameters strictly against their declared type per the [JSON Schema](https://json-schema.org/) specification. For example, a nested parameter typed `"string"` with a `null` value fails validation and blocks the launch.
+
+To leave an optional nested parameter unset, omit the key from your parameters instead of setting it to `null`. Nextflow resolves a missing nested key to `null` at runtime, and your pipeline's conditional logic behaves the same. You can't use nullable types such as `["string", "null"]` in nf-core-style schema files because the nf-schema specification restricts `type` to a single value.
+:::
+
 ### Customize pipeline schema
 
 When the skeleton pipeline schema file has been built with `nf-core schema build`, the command line tool will prompt you to open a [graphical schema editor](https://nf-co.re/pipeline_schema_builder) on the nf-core website.

platform-cloud/docs/troubleshooting_and_faqs/troubleshooting.md

@@ -29,6 +29,23 @@ To resolve:
 
 This error occurs when you execute a DSL1-based Nextflow workflow with [Nextflow 22.03.0-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.03.0-edge) or later.
 
+#### `"<parameter>" must be string` when launching a pipeline
+
+This error occurs when a parameter nested inside an object-typed schema group has a `null` value. Seqera Platform tolerates `null` and blank values for top-level parameters only, and the error message concatenates the group and parameter names. Omit optional nested parameters instead of setting them to `null`:
+
+```yaml
+# Fails validation
+alignment:
+  aligner: bwa
+  reference: null
+
+# Passes validation
+alignment:
+  aligner: bwa
+```
+
+Nextflow resolves a missing key to `null` at runtime, and your pipeline logic behaves the same. For more information, see [Pipeline schema](../pipeline-schema/overview).
+
 #### Sleep commands in Nextflow workflows
 
 The behavior of `sleep` commands in your Nextflow workflows depends on where they are used:

platform-enterprise_docs/pipeline-schema/overview.md

@@ -21,6 +21,12 @@ When you run the `nf-core schema build` command in your pipeline root directory,
 The nf-core community creates the schema builder but it can be used with any Nextflow pipeline.
 :::
 
+:::note Null and blank parameter values
+When you launch a pipeline, the launch form validates your parameters against the pipeline schema and blocks the launch if validation fails. Seqera Platform removes top-level parameters with `null` or blank values before validation. This handling doesn't apply to parameters nested inside object-typed groups, such as `params.alignment.reference`. The launch form validates nested parameters strictly against their declared type per the [JSON Schema](https://json-schema.org/) specification. For example, a nested parameter typed `"string"` with a `null` value fails validation and blocks the launch.
+
+To leave an optional nested parameter unset, omit the key from your parameters instead of setting it to `null`. Nextflow resolves a missing nested key to `null` at runtime, and your pipeline's conditional logic behaves the same. You can't use nullable types such as `["string", "null"]` in nf-core-style schema files because the nf-schema specification restricts `type` to a single value.
+:::
+
 ### Customize pipeline schema
 
 When the skeleton pipeline schema file has been built with `nf-core schema build`, the command line tool will prompt you to open a [graphical schema editor](https://nf-co.re/pipeline_schema_builder) on the nf-core website.

platform-enterprise_docs/troubleshooting_and_faqs/troubleshooting.md

@@ -2,7 +2,7 @@
 title: "General"
 description: "Troubleshooting Seqera Platform"
 date created: "2023-04-23"
-last updated: "2026-07-16"
+last updated: "2026-08-11"
 tags: [troubleshooting, help]
 ---
 
@@ -45,6 +45,23 @@ Verify the following:
 
 This error occurs when you execute a DSL1-based Nextflow workflow with [Nextflow 22.03.0-edge](https://github.com/nextflow-io/nextflow/releases/tag/v22.03.0-edge) or later.
 
+#### `"<parameter>" must be string` when launching a pipeline
+
+This error occurs when a parameter nested inside an object-typed schema group has a `null` value. Seqera Platform tolerates `null` and blank values for top-level parameters only, and the error message concatenates the group and parameter names. Omit optional nested parameters instead of setting them to `null`:
+
+```yaml
+# Fails validation
+alignment:
+  aligner: bwa
+  reference: null
+
+# Passes validation
+alignment:
+  aligner: bwa
+```
+
+Nextflow resolves a missing key to `null` at runtime, and your pipeline logic behaves the same. For more information, see [Pipeline schema](../pipeline-schema/overview).
+
 #### Sleep commands in Nextflow workflows
 
 The behavior of `sleep` commands in your Nextflow workflows depends on where they are used: