Added 'none' to assembler and caller lists so the variant calling and…

… assembly first steps can be run without performing VC or assembly processes.

main.nf

@@ -150,13 +150,13 @@ if (params.protocol == 'amplicon' && !params.skip_variants && !params.amplicon_b
 }
 if (params.amplicon_bed) { ch_amplicon_bed = file(params.amplicon_bed, checkIfExists: true) }
 
-callerList = [ 'varscan2', 'ivar', 'bcftools']
+callerList = [ 'varscan2', 'ivar', 'bcftools', 'none']
 callers = params.callers ? params.callers.split(',').collect{ it.trim().toLowerCase() } : []
 if ((callerList + callers).unique().size() != callerList.size()) {
     exit 1, "Invalid variant calller option: ${params.callers}. Valid options: ${callerList.join(', ')}"
 }
 
-assemblerList = [ 'spades', 'metaspades', 'unicycler', 'minia' ]
+assemblerList = [ 'spades', 'metaspades', 'unicycler', 'minia', 'none' ]
 assemblers = params.assemblers ? params.assemblers.split(',').collect{ it.trim().toLowerCase() } : []
 if ((assemblerList + assemblers).unique().size() != assemblerList.size()) {
     exit 1, "Invalid assembler option: ${params.assemblers}. Valid options: ${assemblerList.join(', ')}"