processDir directive does not resolve variables in the process scope

[heuermh]

transform.nf:

#!/usr/bin/env nextflow

params.dir = "${baseDir}/example"

bamFiles = "${params.dir}/**.bam"
bams = Channel.fromPath(bamFiles).map { path -> tuple(path.baseName, path.toRealPath().getParent(), path) }

process transform {
  publishDir parent, mode: 'copy'

  input:
    set sample, parent, file(bam) from bams
  output:
    set sample, parent, file("${sample}.adam") into reads

  """
  adam-submit transform -force_load_bam $bam ${sample}.adam
  """
}

$ nextflow run transform.nf -with-docker heuermh/adam
N E X T F L O W  ~  version 0.16.0
Launching transform.nf
ERROR ~ Not such variable: parent

 -- Check script 'transform.nf' at line: 10 or see '.nextflow.log' file for more details

[pditommaso]

The above commit solve the problem. However note that like other directives in order to access process local variables they must be enclosed by a closure or dynamic string. For example:

 publishDir "$parent", mode: 'copy'   

[heuermh]

Thanks!

Is there any difference between "$parent" and "${parent}"?
And then by closure, would just publishDir { parent }, mode: 'copy' work?

[pditommaso]

No, both "$parent" and "${parent}" are GString objects.

Yes, the syntax publishDir { parent }, mode: 'copy' should work as well.

[pditommaso]

let me know if it's fixed on your side as well.

[heuermh]

Will do, thank you!