Add ability to provide custom defaults for publishDir directive via config file

[pditommaso]

This ticket aims to provide the ability to custom default settings for the publishDir directive via the nextflow.config file.

The default settings should be provided using the nextflow.defaults.publishDir configuration scope. For example:

nextflow {
  defaults {
    publishDir = [mode: 'copy', enabled: false]
  }
}

When provided, they should override the built-in default settings and applied when creating a PublishDir instance.

[bentsherman]

@pditommaso you closed a bunch of issues and PRs about supporting closures for these fields, so do you intend for these default settings to support closures in some way? Otherwise it isn't really addressed those other issues. In many cases they want to configure the PublishDir with task-specific inputs which requires closures.

[bentsherman]

If the publishDir directive can be specified in the pipeline code (#4375), then you could instead use a function to provide defaults:

def publishDir(path, opts=[:]) {
  final defaults = [
    path: params.outdir,
    mode: params.publish_mode
  ]
  defaults + [path: path] + opts
}

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[bentsherman]

This convenience is no longer needed once the workflow output DSL #4784 is implemented

[bentsherman]

Closing in favor of the output i.e. "publish" DSL and #4839 which provides some config options for publish retry strategy

[pditommaso]

Not 100% this should be thrown away