set publishDir mode based on config

[kelly-sovacool]

It would be handy to set the publishDir mode based on a parameter, e.g.

in the process:

publishDir "$params.outdir/$sample_id", mode: "$params.filePublishMode"

in nextflow.config:

params {
    filePublishMode: 'copy'
    adapters = '/opt2/TruSeq_and_nextera_adapters.consolidated.fa'
}

However, this does not work

ERROR ~ Error executing process > 'FASTQC_RAW (SRR1822157_1)'

Caused by:
  No enum constant nextflow.processor.PublishDir.Mode.NULL


 -- Check '.nextflow.log' file for details

The docs state that mode must be a string literal, i.e. it cannot be a parameter.
The Nextflow team is aware and appears to have plans to make it possible to set the mode and other publishDir options in the config file. Once they implement it we can update our usage too.

See nextflow-io/nextflow#4186

[vinegang]

Give this a try
filePublishMode = "copy"

[kelly-sovacool]

that fixed it, thanks @vinegang!

[kelly-sovacool]

fixed by 79eefdf