Document params-file and improve self-update

[abhi18av]

Updated the documentation for --params-file and self-update

[bentsherman]

The params file can be YAML or JSON. I would say YAML/JSON file instead of YML file.

[bentsherman]

Also @pditommaso we should clarify what happens if you provide params through a config file and a params file via CLI arguments. I think the params file takes priority but I'm not certain.

[abhi18av]

Yes, this question has come up recently #2662

[pditommaso]

Was missing this conversation. The CLI params overrides the ones the json/yaml file.

You can see it here, it reads the params file and put it into the result map. then if there are cli params copy them over the result map.

nextflow/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

Lines 496 to 513 in 0f63f1a

	final result = [:]
	final file = getParamsFile()
	if( file ) {
	def path = validateParamsFile(file)
	def type = path.extension.toLowerCase() ?: null
	if( type == 'json' )
	readJsonFile(path, configVars, result)
	else if( type == 'yml' || type == 'yaml' )
	readYamlFile(path, configVars, result)
	}
	// set the CLI params
	if( !params )
	return result
	for( Map.Entry<String,String> entry : params ) {
	addParam( result, entry.key, entry.value )
	}

[abhi18av]

Accomodate Ben's review about the JSON optoin.

[pditommaso]

Ok, updated it removing the refence to the NXF_VER. Eventually it could be added into a tip section