Workflow introspection

Runtime metadata

The implicit workflow object allows you to access some workflow and runtime metadata in your Nextflow scripts. For example:

println "Project : $workflow.projectDir"
println "Git info: $workflow.repository - $workflow.revision [$workflow.commitId]"
println "Cmd line: $workflow.commandLine"
println "Manifest's pipeline version: $workflow.manifest.version"

Tip

To shortcut the access to multiple workflow properties you can use the Groovy with method.

The following table lists the properties that can be accessed on the workflow object:

Name

Description

scriptId

Project main script unique hash ID.

scriptName

Project main script file name.

scriptFile

Project main script file path.

repository

Project repository Git remote URL.

commitId

Git commit ID of the executed workflow repository.

revision

Git branch/tag of the executed workflow repository.

projectDir

Directory where the workflow project is stored in the computer.

launchDir

Directory where the workflow execution has been launched.

workDir

Workflow working directory.

homeDir

User system home directory.

userName

User system account name.

configFiles

Configuration files used for the workflow execution.

container

Docker image used to run workflow tasks. When more than one image is used it returns a map object containing [process name, image name] pair entries.

containerEngine

Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.

commandLine

Command line as entered by the user to launch the workflow execution.

profile

Used configuration profile.

runName

Mnemonic name assigned to this execution instance.

sessionId

Unique identifier (UUID) associated to current execution.

resume

Returns true whenever the current instance is resumed from a previous execution.

start

Timestamp of workflow at execution start.

manifest

Entries of the workflow manifest.

complete

Timestamp of workflow when execution is completed.

duration

Time elapsed to complete workflow execution.

* success

Reports if the execution completed successfully.

* exitStatus

Exit status of the task that caused the workflow execution to fail.

* errorMessage

Error message of the task that caused the workflow execution to fail.

* errorReport

Detailed error of the task that caused the workflow execution to fail.

Properties marked with a are accessible only in the workflow completion handler.
Properties marked with a * are accessible only in the workflow completion and error handlers. See the Completion handler section for details.

Nextflow metadata

The implicit nextflow object allows you to access the metadata information of the Nextflow runtime.

Name

Description

nextflow.version

Nextflow runtime version number.

nextflow.build

Nextflow runtime build number.

nextflow.timestamp

Nextflow runtime compile timestamp.

The method nextflow.version.matches allows you to check if the Nextflow runtime satisfies the version requirement eventually needed by your workflow script. The required version string can be prefixed with the usual comparison operators eg >, >=, =, etc. or postfixed with the + operator to specify a minimal version requirement. For example:

if( !nextflow.version.matches('0.22+') ) {
    println "This workflow requires Nextflow version 0.22 or greater -- You are running version $nextflow.version"
    exit 1
}

Completion handler

Due to the asynchronous nature of Nextflow the termination of a script does not correspond to the termination of the running workflow. Thus some information, only available on execution completion, needs to be accessed by using an asynchronous handler.

The onComplete event handler is invoked by the framework when the workflow execution is completed. It allows one to access the workflow termination status and other useful information. For example:

workflow.onComplete {
    println "Pipeline completed at: $workflow.complete"
    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
}

If you want an e-mail notification on completion, check Mail & Notifications.

Error handler

The onError event handler is invoked by Nextflow when a runtime or process error caused the pipeline execution to stop. For example:

workflow.onError {
    println "Oops... Pipeline execution stopped with the following message: ${workflow.errorMessage}"
}

Note

Both the onError and onComplete handlers are invoked when an error condition is encountered. However the first is called as soon as the error is raised, while the second just before the pipeline execution is going terminate. When using the finish errorStrategy, between the two there could be a significant time gap depending by the time required to complete any pending job.

Decoupling metadata

The workflow event handlers can be defined also in the nextflow.config file. This is useful to decouple the handling of pipeline events from the main script logic.

When the event handlers are included in a configuration file the only difference is that the onComplete and the onError closures have to be defined by using the assignment operator as shown below:

workflow.onComplete = {
    // any workflow property can be used here
    println "Pipeline complete"
    println "Command line: $workflow.commandLine"
}


workflow.onError = {
    println "Oops .. something when wrong"
}

Note

It is possible to define a workflow event handlers both in the pipeline script and in the configuration file.