Replace params.modules with PublishDir and process.ext settings.

[mahesh-panchal]

Feature request: Replace params.modules with publishDir and ext.

This issue is a collection point for discussions on various topics regarding nf-core/rnaseq#701.

Is your feature request related to a problem? Please describe

PublishDir and tool arg configuration is distributed in many places in the nf-core workflows.
Using publishDir and process selectors could remedy file publishing configuration to be in one place.
Using ext.args and process selectors could provide tool parameters configuration in one place.

Describe the solution you'd like

nf-core/rnaseq#701 shows it implemented in the nf-core rnaseq workflow.

Current discussion points:

• Using custom functions in nextflow.config: Prototype implementation for new Nextflow native DSL2 syntax on nf-core rnaseq#701 (comment)
• How to proceed with ext.args changes not triggering reruns:Prototype implementation for new Nextflow native DSL2 syntax on nf-core rnaseq#701 (comment)
• How to lint publishDir directives: Prototype implementation for new Nextflow native DSL2 syntax on nf-core rnaseq#701 (comment)

TODO list

• Updating nf-core/modules
• Update module template
  • Remove/Amend function import
  • Remove options
  • Use Jinja to write versions.yml process names
  • Remove publishDir.
• Update pipeline template
• lib/ (if keeping getSoftwareName, getProcessName).
• Update linter to check for mode: params.publish_dir_mode.
• Update linter to check for enabled:false, pattern: , or saveAs: { filename -> filename.equals('versions.yml') ? null : filename } so versions.yml is not published along with module outputs.
• Update tests to use publishDir in config and remove NF_CORE_MODULES_TEST=1 env.

[mahesh-panchal]

Added update of what removing functions.nf would look like here: https://github.com/mahesh-panchal/rnaseq/pull/1

[drpatelh]

Created individual issues for these @mahesh-panchal so we can track and discuss on them separately.

#1285
#1286
#1287