Update docs

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

docs/cli.md

@@ -269,49 +269,42 @@ See {ref}`cli-secrets` for more information.
 :::{versionadded} 26.04.0
 :::
 
-Module management commands enable working with reusable, registry-based modules. The Nextflow module system allows you to install, run, search, and publish standardized modules from registries, eliminating duplicate work and spreading improvements throughout the community.
+The `module` command enables working with reusable, registry-based modules. The Nextflow module system allows you to install, run, search, and publish standardized modules from registries, eliminating duplicate work and sharing improvements with the community.
 
 Use these commands to discover modules in registries, install them into your project, run them directly without creating a workflow, and publish your own modules for others to use.
 
-### Installing modules
+### Searching for modules
 
-The `module install` command downloads modules from a registry and makes them available in your workflow. Modules are stored locally in the `modules/` directory. An additional `.module-info` file is created during to store installation information such as the module checksum at installation and the registry URL.
+The `module search` command queries the module registry to discover available modules by keyword or name.
 
-Use this to add reusable modules to your pipeline, manage module versions, or update modules to newer versions.
+Use this to find modules for specific tasks, explore available tools, or discover community modules.
 
 ```console
-$ nextflow module install nf-core/fastqc
-$ nextflow module install nf-core/fastqc -version 1.0.0
+$ nextflow module search alignment
+$ nextflow module search "quality control" -limit 10
+$ nextflow module search bwa -output json
 ```
 
-After installation, module will be available in `modules/nf-core/fastqc`.
+Results include module names, versions, descriptions, and download statistics. Use `-limit` to control the number of results and `-output json` for JSON-formatted output.
 
-Use the `-force` flag to reinstall a module even if local modifications exist.
-
-See {ref}`cli-module-install` for more information.
+See {ref}`cli-module-search` for more information.
 
-### Running modules directly
+### Installing modules
 
-The `module run` command executes a module directly from the registry without requiring a wrapper workflow. This provides immediate access to module functionality for ad-hoc tasks or testing.
+The `module install` command downloads modules from a registry and makes them available in your workflow. Modules are stored locally in the `modules/` directory. An additional `.module-info` file is created during to store installation information such as the module checksum at installation and the registry URL.
 
-Use this to quickly run a module, test module functionality, or execute one-off data processing tasks.
+Use this to add reusable modules to your pipeline, manage module versions, or update modules to newer versions.
 
 ```console
-$ nextflow module run nf-core/fastqc --input 'data/*.fastq.gz'
-$ nextflow module run nf-core/fastqc --input 'data/*.fastq.gz' -version 1.0.0
+$ nextflow module install nf-core/fastqc
+$ nextflow module install nf-core/fastqc -version 1.0.0
 ```
 
-The command accepts all standard Nextflow execution options (`-profile`, `-resume`, etc.):
+The installed module will be available in `modules/nf-core/fastqc`.
 
-```console
-$ nextflow module run nf-core/salmon \
-    --reads reads.fq \
-    --index salmon_index \
-    -profile docker \
-    -resume
-```
+Use the `-force` flag to reinstall a module even if local modifications exist.
 
-See {ref}`cli-module-run` for more information.
+See {ref}`cli-module-install` for more information.
 
 ### Listing modules
 
@@ -324,26 +317,10 @@ $ nextflow module list
 $ nextflow module list -output json
 ```
 
-The output shows each module's name, installed version, and whether it has been modified locally. Use `-json` for machine-readable output suitable for scripting.
+The output shows each module's name, installed version, and whether it has been modified locally. Use `-o json` for JSON-formatted output.
 
 See {ref}`cli-module-list` for more information.
 
-### Searching for modules
-
-The `module search` command queries the module registry to discover available modules by keyword or name.
-
-Use this to find modules for specific tasks, explore available tools, or discover community contributions.
-
-```console
-$ nextflow module search alignment
-$ nextflow module search "quality control" -limit 10
-$ nextflow module search bwa -output json
-```
-
-Results include module names, versions, descriptions, and download statistics. Use `-limit` to control the number of results and `-output json` for programmatic access.
-
-See {ref}`cli-module-search` for more information.
-
 ### Viewing module information
 
 The `module info` command displays detailed metadata and usage information for a specific module from the registry.
@@ -360,6 +337,31 @@ The output includes the module's version, description, authors, keywords, tools,
 
 See {ref}`cli-module-info` for more information.
 
+### Running modules directly
+
+The `module run` command executes a module directly from the registry without requiring a wrapper workflow. This provides immediate access to module functionality for ad-hoc tasks or testing.
+
+Use this to quickly run a module, test module functionality, or execute one-off data processing tasks.
+
+```console
+$ nextflow module run nf-core/fastqc --input 'data/*.fastq.gz'
+$ nextflow module run nf-core/fastqc --input 'data/*.fastq.gz' -version 1.0.0
+```
+
+The command accepts all standard Nextflow execution options (`-profile`, `-resume`, etc.):
+
+```console
+$ nextflow module run nf-core/salmon \
+    --reads reads.fq \
+    --index salmon_index \
+    -profile docker \
+    -resume
+```
+
+Process inputs can be specified like params on the command line. For example, `--reads reads.fq` corresponds to the `reads` input in the `nf-core/salmon` module. Run `nextflow module info nf-core/salmon` to see the available params for the module.
+
+See {ref}`cli-module-run` for more information.
+
 ### Removing modules
 
 The `module remove` command deletes modules from your project, removing local files and configuration entries.
@@ -386,7 +388,7 @@ $ nextflow module publish myorg/my-module
 $ nextflow module publish myorg/my-module -dry-run
 ```
 
-Publishing requires authentication via the `NXF_REGISTRY_TOKEN` environment variable or `registry.apiKey` in the Nextflow configuration. The module must include `main.nf`, `meta.yml`, and `README.md` files.
+Publishing requires authentication via the `NXF_REGISTRY_TOKEN` environment variable or the `registry.apiKey` config option. The module must include `main.nf`, `meta.yml`, and `README.md` files.
 
 Use `-dry-run` to validate your module structure without uploading.
 

docs/module.md

@@ -293,7 +293,7 @@ Modules are designed to be easy to share and re-use across different pipelines,
 :::{versionadded} 26.04.0
 :::
 
-Nextflow provides a module registry that enables you to install, share, and manage modules from centralized registries. This system provides version management, integrity checking, and seamless integration with the Nextflow DSL.
+Nextflow provides a module registry that enables you to install, publish, and manage modules from centralized registries. This system provides version management, integrity checking, and seamless integration with the Nextflow language.
 
 ### Installing modules from a registry
 
@@ -323,8 +323,7 @@ For ad-hoc tasks or testing, you can run a module directly without creating a wo
 $ nextflow module run nf-core/fastqc --input 'data/*.fastq.gz'
 ```
 
-This command accepts all standard Nextflow options (`-profile`, `-resume`, etc.) and automatically downloads the module if not already installed.
-
+This command accepts all standard `nextflow run` options (`-profile`, `-resume`, etc.) and automatically downloads the module if not already installed.
 
 ### Discovering modules
 
@@ -374,7 +373,7 @@ $ nextflow module info nf-core/fastqc
 $ nextflow module info nf-core/fastqc -version 1.0.0
 ```
 
-The output includes the module description, authors, keywords, tools, inputs, outputs, and a ready-to-use command-line template. Use `-json` to get machine-readable output.
+The output includes the module description, authors, keywords, tools, inputs, outputs, and a ready-to-use command-line template. Use `-o json` to get machine-readable output.
 
 ### Publishing modules