Simplify logic for staging primer files

main.nf

@@ -26,31 +26,21 @@ if (params.help) {
 /* --        GENOME PARAMETER VALUES           -- */
 ////////////////////////////////////////////////////
 
-def primer_set = ''
+def primer_set         = ''
 def primer_set_version = 0
-if (!params.public_data_ids && params.platform == 'illumina') {
-    if (params.protocol == 'amplicon') {
-        primer_set = params.primer_set
-        primer_set_version = params.primer_set_version
-    }
-} else if (!params.public_data_ids && params.platform == 'nanopore') {
-    if (params.primer_set != 'artic') {
-        log.error "Invalid option: --primer_set '${params.primer_set}'. Only --primer_set 'artic' is supported when running the pipeline on Nanopore input data.\n"
-        System.exit(1)
-    }
-    if (!params.primer_set_version) {
-        log.error "Invalid option: --primer_set_version '${params.primer_set_version}'.\nPlease specify a valid option when using --primer_set '${params.primer_set}'.\n"
-        System.exit(1)
-    }
-    primer_set = params.primer_set
+if (!params.public_data_ids && params.platform == 'illumina' && params.protocol == 'amplicon') {
+    primer_set         = params.primer_set
     primer_set_version = params.primer_set_version
+} else if (!params.public_data_ids && params.platform == 'nanopore') {
+    primer_set          = 'artic'
+    primer_set_version  = params.primer_set_version
+    params.artic_scheme = Workflow.get_genome_attribute(params, 'scheme', log, primer_set, primer_set_version)
 }
 
 params.fasta         = Workflow.get_genome_attribute(params, 'fasta'     , log, primer_set, primer_set_version)
 params.gff           = Workflow.get_genome_attribute(params, 'gff'       , log, primer_set, primer_set_version)
-params.primer_bed    = Workflow.get_genome_attribute(params, 'primer_bed', log, primer_set, primer_set_version)
-params.artic_scheme  = Workflow.get_genome_attribute(params, 'scheme'    , log, primer_set, primer_set_version)
 params.bowtie2_index = Workflow.get_genome_attribute(params, 'bowtie2'   , log, primer_set, primer_set_version)
+params.primer_bed    = Workflow.get_genome_attribute(params, 'primer_bed', log, primer_set, primer_set_version)
 
 ////////////////////////////////////////////////////
 /* --         PRINT PARAMETER SUMMARY          -- */