VS Code integration

The Nextflow VS Code extension provides IDE support for Nextflow pipelines.

Features

Syntax highlighting

The VS Code extension highlights Nextflow scripts and config files for better readability.

Diagnostics

The extension highlights source code in red for errors and yellow for warnings.

To view all diagnostics for the workspace, open the Problems tab. Here, you can search for diagnostics by diagnostic message, filename, and so on.

Note

The language server parses scripts and config files according to the Nextflow language specification, which is more strict than the Nextflow CLI. See Updating Nextflow syntax for more information.

Hover hints

When you hover over certain source code elements, such as variable names and function calls, the extension provides a tooltip with related information, such as the definition and/or documentation for the element.

Code completion

The extension suggests auto-completions for variable names, function names, config settings, and other symbols as you type. The extension also provides several snippets for common script declarations, such as processes and workflows.

Formatting

The extension can format your scripts and config files based on a standard set of formatting rules. Rules can be customized using the Nextflow > Formatting extension settings.

Use the Format Document command in the command palette to format the current file.

Renaming symbols

The extension can rename all references of a symbol (e.g., a workflow, process, function, or variable) throughout the code.

To rename a symbol, right-click the symbol, select Rename Symbol, and enter a new name.

Parameter schema

If a nextflow_schema.json file exists in the same directory as a script with an entry workflow, the extension uses the schema to provide validation, hover hints, and code completion for params in the entry workflow.

DAG preview for workflows

The extension can generate a workflow DAG that includes the workflow inputs, outputs, and any processes or workflows that are called by the selected workflow. The workflow DAG is displayed in a new panel to the side.

To preview the DAG of a workflow, select the Preview DAG CodeLens above the workflow definition.

Note

The Preview DAG CodeLens is only available when the script does not contain any errors.

Troubleshooting

In the event of an error, you can stop or restart the language server from the command palette. See Commands for the set of available commands.

Report issues at nextflow-io/vscode-language-nextflow or nextflow-io/language-server. When reporting, include a minimal code snippet that reproduces the issue and any error logs from the server. To view logs, open the Output tab and select Nextflow Language Server from the dropdown. Enable Nextflow > Debug in the extension settings to show additional log messages while debugging.

Limitations

The language server does not detect certain filesystem changes, such as changing the current Git branch. Restart the language server from the command palette to sync it with your workspace.
The language server does not recognize configuration options from third-party plugins and will report “Unrecognized config option” warnings for them.
The language server provides limited support for Groovy scripts in the lib directory. Errors in Groovy scripts are not reported as diagnostics, and changing a Groovy script does not automatically re-compile the Nextflow scripts that reference it. Edit the Nextflow script or close and re-open it to refresh the diagnostics.

Commands

The following commands are available from the command palette:

Restart language server
Stop language server

Settings

The following settings are available:

nextflow.debug: Enable debug logging and debug information in hover hints.
nextflow.files.exclude: Configure glob patterns for excluding folders from being searched for Nextflow scripts and configuration files.
nextflow.formatting.harshilAlignment: Use the Harshil Alignment™️ when formatting Nextflow scripts and config files.
nextflow.java.home: Specifies the folder path to the JDK. Use this setting if the extension cannot find Java automatically.
nextflow.paranoidWarnings: Enable additional warnings for future deprecations, potential problems, and other discouraged patterns.

Language server

Most of the functionality of the VS Code extension is provided by the Nextflow language server, which implements the Language Server Protocol (LSP) for Nextflow scripts and config files.

The language server is distributed as a standalone Java application. It can be integrated with any editor that functions as an LSP client. Currently, only the VS Code integration is officially supported, but community contributions for other editors are welcome.