Allow closure type as input in PublishDir.setMode()

[dwishsan]

Hi everyone !

First of all, a big THANK YOU for nextflow, it is very handy :)

Some context on my feature request

I am using nextflow with configuration files to customize processes.
This mean, among other things, that I DO NOT define the publishDir directive for each process, like what is done in the nextflow documentation, I rather define the publishDir {} one and one time only for all processes (in a process {} directive) using a closure for the publisDir.path.
This is very handy and it works very well!

But recently, I wanted to add the possibility to copy the published files instead of doing symlinks (the default). In theory, this is very easy to do, I just have to set publishDir.mode with the wanted closure.

But I get this error:
Invalid method invocation 'setMode' with arguments: (Script989C00012DEDEFE63A87A761299AE910$_run_closure6$_closure56) on PublishDir type

Indeed, in the code, PublishDir.setMode() can take either a nextflow.processor.PublishDir.Mode or a String, but not a closure.

New feature

Add a setMode(def value) method for the PublishDir class.

Usage scenario

I do not know if other individuals are using closure to set their publishDir.path, but it would be very helpfull for me if this feature is added in Nextflow :)

Suggest implementation

I THINK this should work:

void setMode( Closure value ) {
  setMode(value.call())
}

Best,
Audric

[dwishsan]

I just realised that publishDir.enabled does not work with closures either. A workarround, suggested here: #3692, could be to set publishDir.path to null, but this is not allowed by Nextflow (Path string cannot be empty). This is due to the following piece of code:

void apply( Set<Path> files, TaskRun task ) {

        if( !files || !enabled )
            return

        if( !path )
            throw new IllegalStateException("Target path for directive publishDir cannot be null")

        if( nullPathWarn )
            log.warn "Process `$task.processor.name` publishDir path contains a variable with a null value"

        this.sourceDir = task.targetDir
        this.sourceFileSystem = sourceDir.fileSystem
        this.stageInMode = task.config.stageInMode
        this.taskName = task.name

        apply0(files)
    }

But it could be replaced by this in order to work, if there is not particular reason why the publishDir.path can not be null:

void apply( Set<Path> files, TaskRun task ) {

        if( !files || !enabled || !path)
            return

        if( nullPathWarn )
            log.warn "Process `$task.processor.name` publishDir path contains a variable with a null value"

        this.sourceDir = task.targetDir
        this.sourceFileSystem = sourceDir.fileSystem
        this.stageInMode = task.config.stageInMode
        this.taskName = task.name

        apply0(files)
    }

I was wondering: is there any reason for the publishDir directives (except path and saveAs) to not accept closures as input?
Shouldn't all of them accept closures?

[pditommaso]

Thanks for the suggestion. No plan to support this in the short term. We are working to a better why to define publishDir defaults #4186