Add pipeline linting for configuration files such that all directives which use `params` are closures.

[mahesh-panchal]

Description of feature

From slack: It's still common that users want to supply parameters using -c. This often leads to users encountering this issue: https://github.com/nextflow-io/nextflow/issues/2662.

From the developer side, one change we can make is that all process directives which use params should be nested in a closure. E.g.

• ext.args = "$params.something" -> ext.args = { "$params.something" }.
• ext.prefix = "$params.something" -> ext.prefix = { "$params.something" }.
• publishDir = [ path: ".../$params.something", mode: params.publish_dir_mode ] -> publishDir = [ path: { ".../$params.something" } , mode: params.publish_dir_mode ]

mode: of publishDir doesn't accept a closure, so should be the only case ignored.

There are some cases of using params in enabled: of publishDir (eg. rnaseq) which also doesn't evaluate closures. These should be linted to move the enabled: test into saveAs: to allow closures.

[mahesh-panchal]

It's seems there are some parameters used outside the process directive scope in the nextflow.config and these must be passed on the command-line or with a -params-file.

• params.outdir: used in timeline, trace, report, and dag.
• params.max_time: used in check_max function.
• params.max_memory: used in check_max function.
• params.max_cpus: used in check_max function.
• params.genomes: used in nextflow.config.
• params.igenomes_ignore: used in nextflow.config.
• params.igenomes_base: used in igenomes.config.