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"

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.
^✝ 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' }"
}

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.

Notification message¶

Nextflow does not provide a built-in mechanism to send emails or other messages. However the mail standard Linux tool (or an equivalent one) can easily be used to send a notification message when the workflow execution is completed, as shown below:

workflow.onComplete {
    def subject = 'My pipeline execution'
    def recipient = 'me@gmail.com'

    ['mail', '-s', subject, recipient].execute() << """

    Pipeline execution summary
    ---------------------------
    Completed at: ${workflow.complete}
    Duration    : ${workflow.duration}
    Success     : ${workflow.success}
    workDir     : ${workflow.workDir}
    exit status : ${workflow.exitStatus}
    Error report: ${workflow.errorReport ?: '-'}
    """
}

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.