Split standard library docs into multiple pages

docs/cache-and-resume.md

@@ -16,7 +16,7 @@ The task cache is used in conjunction with the [work directory](#work-directory)
 
 The task hash is computed from the following metadata:
 
-- Session ID (see `workflow.sessionId` in {ref}`stdlib-constants`)
+- Session ID (see `workflow.sessionId` in the {ref}`stdlib-namespaces-workflow` namespace)
 - Task name (see `name` in {ref}`trace-report`)
 - Task container image (if applicable)
 - Task {ref}`environment modules <process-module>` (if applicable)

docs/developer/nextflow.md

@@ -14,7 +14,7 @@ Some classes may be excluded from the above diagram for brevity.
 
 ## Notes
 
-The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`stdlib-functions` for details.
+The `Nextflow` class implements several methods that are exposed to Nextflow scripts. See {ref}`stdlib-namespaces-global` for details.
 
 The `Channel` class implements the channel factory methods, and it is exposed directly to Nextflow scripts. See {ref}`channel-page` for details.
 

docs/reference/process.md

@@ -630,7 +630,7 @@ The following error strategies are available:
 
 `ignore`
 : When a task fails, ignore it and continue the pipeline execution. If the `workflow.failOnIgnore` config option is set to `true`, the pipeline will report an error (i.e. return a non-zero exit code) upon completion. Otherwise, the pipeline will complete successfully.
-: See {ref}`stdlib-constants` for more information on `workflow.failOnIgnore`.
+: See the {ref}`stdlib-namespaces-workflow` namespace for more information.
 
 `retry`
 : When a task fails, retry it.

docs/reference/stdlib-groovy.md

@@ -0,0 +1,25 @@
+(stdlib-groovy)=
+
+# Groovy and Java classes
+
+Any Groovy or Java class that is available to Nextflow at runtime can be used in a Nextflow script. The following classes are imported by default:
+
+- `groovy.lang.*`
+- `groovy.util.*`
+- `java.io.*`
+- `java.lang.*`
+- `java.math.BigDecimal`
+- `java.math.BigInteger`
+- `java.net.*`
+- `java.util.*`
+
+All other classes must be referenced by their fully-qualified name:
+
+```nextflow
+def vals = [1, 2, 3]
+println groovy.json.JsonOutput.toJson(vals)
+```
+
+:::{note}
+The set of classes in Nextflow's runtime classpath can change between different Nextflow versions. As a best practice, any code that uses classes outside the Nextflow standard library should either be refactored to only use the Nextflow standard library or be refactored as a {ref}`plugin <plugins-dev-page>` with explicit dependencies.
+:::

docs/reference/stdlib-namespaces.md

@@ -0,0 +1,272 @@
+(stdlib-namespaces)=
+
+# Namespaces
+
+This page lists all of the available namespaces in the Nextflow standard library.
+
+(stdlib-namespaces-global)=
+
+## Global namespace
+
+The global namespace contains globally available constants and functions.
+
+**Constants**
+
+`baseDir: Path`
+: :::{deprecated} 20.04.0
+  :::
+: Alias of `workflow.projectDir`.
+
+`launchDir: Path`
+: Alias of `workflow.launchDir`.
+
+`moduleDir: Path`
+: Directory where a module script is located (equivalent to `projectDir` if used in the main script).
+
+`params`
+: Map of workflow parameters specified in the config file or as command line options.
+
+`projectDir: Path`
+: Alias of `workflow.projectDir`.
+
+`secrets: Map<String,String>`
+: :::{versionadded} 24.02.0-edge
+  :::
+: Map of pipeline secrets. See {ref}`secrets-page` for more information.
+
+`workDir: Path`
+: Alias of `workflow.workDir`.
+
+**Functions**
+
+`branchCriteria( criteria: Closure ) -> Closure`
+: Create a branch criteria to use with the {ref}`operator-branch` operator.
+
+`env( name: String ) -> String`
+: :::{versionadded} 24.11.0-edge
+  :::
+: Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
+`error( message: String = null )`
+: Throw a script runtime error with an optional error message.
+
+`exit( exitCode: int = 0, message: String = null )`
+: :::{deprecated} 22.06.0-edge
+  Use `error()` instead
+  :::
+: Stop the pipeline execution and return an exit code and optional error message.
+
+`file( filePattern: String, [options] ) -> Path | List<Path>`
+: Get a file from a file name or glob pattern. Returns a collection of files if the glob pattern yields zero or multiple files.
+
+: The following options are available:
+
+  `checkIfExists: boolean`
+  : When `true`, throws an exception if the specified path does not exist in the file system (default: `false`)
+
+  `followLinks: boolean`
+  : When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`)
+
+  `glob: boolean`
+  : When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
+
+  `hidden: boolean`
+  : When `true`, includes hidden files in the resulting paths (default: `false`)
+
+  `maxDepth: int`
+  : Maximum number of directory levels to visit (default: *no limit*)
+
+  `type: String`
+  : Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
+
+: See also: {ref}`Channel.fromPath <channel-path>`.
+
+`files( filePattern: String, [options] ) -> List<Path>`
+: Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.
+
+`groupKey( key, size: int ) -> GroupKey`
+: Create a grouping key to use with the {ref}`operator-grouptuple` operator.
+
+`multiMapCriteria( criteria: Closure ) -> Closure`
+: Create a multi-map criteria to use with the {ref}`operator-multiMap` operator.
+
+`print( value )`
+: Print a value to standard output.
+
+`printf( format: String, values... )`
+: Print a formatted string with the given values to standard output.
+
+`println( value )`
+: Print a value to standard output with a newline.
+
+`sendMail( [options] )`
+: Send an email. See {ref}`mail-page` for more information.
+
+`sleep( milliseconds: long )`
+: Sleep for the given number of milliseconds.
+
+`tuple( collection: List ) -> ArrayTuple`
+: Create a tuple object from the given collection.
+
+`tuple( args... ) -> ArrayTuple`
+: Create a tuple object from the given arguments.
+
+(stdlib-namespaces-channel)=
+
+## `channel`
+
+The `channel` namespace contains the built-in channel factories. See {ref}`channel-factory` for details.
+
+(stdlib-namespaces-nextflow)=
+
+## `nextflow`
+
+The `nextflow` namespace contains information about the current Nextflow runtime.
+
+`build: int`
+: Nextflow runtime build number.
+
+`timestamp: String`
+: Nextflow runtime compile timestamp.
+
+`version: VersionNumber`
+: Nextflow runtime version number. See {ref}`VersionNumber <stdlib-types-versionnumber>` for more information.
+
+(stdlib-namespaces-workflow)=
+
+## `workflow`
+
+The `workflow` namespace contains information about the current workflow run.
+
+**Properties**
+
+`commandLine: String`
+: Command line as entered by the user to launch the workflow execution.
+
+`commitId: String`
+: Git commit ID of the executed workflow repository.
+: When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
+
+`complete: OffsetDateTime`
+: *Available only in the `workflow.onComplete` handler*
+: Timestamp of workflow when execution is completed.
+
+`configFiles: List<Path>`
+: Configuration files used for the workflow execution.
+
+`container: String | Map<String,String>`
+: Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.
+
+`containerEngine: String`
+: Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
+
+`duration: Duration`
+: *Available only in the `workflow.onComplete` handler*
+: Time elapsed to complete workflow execution.
+
+`errorMessage: String`
+: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+: Error message of the task that caused the workflow execution to fail.
+
+`errorReport: String`
+: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+: Detailed error of the task that caused the workflow execution to fail.
+
+`exitStatus: int`
+: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+: Exit status of the task that caused the workflow execution to fail.
+
+`failOnIgnore: boolean`
+: :::{versionadded} 24.05.0-edge
+  :::
+: Whether the `workflow.failOnIgnore` config option was enabled.
+: See also: {ref}`process-error-strategy`
+
+`fusion`
+: Namespace containing information about the current Fusion runtime. The following properties are available:
+
+: `enabled: boolean`
+  : Whether Fusion is enabled.
+
+: `version: String`
+  : The Fusion version being used.
+
+`homeDir: Path`
+: User system home directory.
+
+`launchDir: Path`
+: Directory where the workflow was launched.
+
+`manifest`
+: Namespace corresponding to the {ref}`config-manifest` config scope.
+
+`outputDir: Path`
+: :::{versionadded} 24.10.0
+  :::
+: Workflow output directory.
+
+`preview: boolean`
+: :::{versionadded} 24.04.0
+  :::
+: Whether the current workflow run is a preview run.
+
+`profile: String`
+: Comma-separated list of active configuration profiles.
+
+`projectDir: Path`
+: Directory where the workflow project is located.
+
+`repository: String`
+: Project repository Git remote URL.
+
+`resume: boolean`
+: Returns `true` whenever the current instance is resumed from a previous execution.
+
+`revision: String`
+: Git branch/tag of the executed workflow repository.
+: When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
+
+`runName: String`
+: Mnemonic name assigned to this execution instance.
+
+`scriptFile: Path`
+: Project main script file path.
+
+`scriptId: String`
+: Project main script unique hash ID.
+
+`scriptName: String`
+: Project main script file name.
+
+`sessionId: UUID`
+: Unique identifier (UUID) associated to current execution.
+
+`start: OffsetDateTime`
+: Timestamp of workflow at execution start.
+
+`stubRun: boolean`
+: Returns `true` whenever the current instance is a stub-run execution .
+
+`success: boolean`
+: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
+: Reports if the execution completed successfully.
+
+`userName: String`
+: User system account name.
+
+`wave`
+: Namespace containing Wave runtime information. The following properties are available:
+
+: `enabled: boolean`
+  : Whether Wave is enabled.
+
+`workDir: Path`
+: The directory where task temporary files are stored.
+
+**Functions**
+
+`onComplete( action: Closure )`
+: Define an action to take when the workflow completes (whether successful or not).
+
+`onError( action: Closure )`
+: Define an action to take if the workflow is terminated due to a runtime error or task failure.