Rename --mode to --library

[nsyzrantsev]

The --mode <rnaseq/amplicon> falg should be renamed to --library <rnaseq/amplicon>.

Also don't forget to fix a nextflow.config:

pyigmap/nextflow.config

Lines 62 to 90 in 1f1df84

	def getFiltersList() {
	def filtersList = []
	if (params.remove_chimeras) {
	filtersList << "--remove-chimeras"
	}
	if (params.fq1_barcode_pattern == null && params.fq2_barcode_pattern == null) {
	filtersList << "--top-c-call --top-v-alignment-call"
	}
	if (params.only_best_alignment) {
	filtersList << "--only-best-alignment"
	}
	if (params.discard_junctions_with_N) {
	filtersList << "--discard-junctions-with-N"
	}
	if (params.fq1_barcode_pattern != null || params.fq2_barcode_pattern != null) {
	filtersList << "--skip-pgen-calculation"
	} else if (params.filter_pgen_all != null) {
	filtersList << "--filter-pgen-all ${params.filter_pgen_all}"
	} else {
	filtersList << "--filter-pgen-singletons ${params.filter_pgen_singletons}"
	}
	return filtersList
	}