Add lncRNA as valid gene_type

Fixes a bug where all long non-coding RNAs were removed from Ensembl 105, because the gene type had been renamed from lincRNA to lncRNA.

bin/normalisation/normaliseCountMatrix.R

@@ -146,7 +146,7 @@ if (filter_qc){
  message("## Filter SummarizedExperiment by removing samples that fail QC ##")
 
  #Specify valid chromsomes and valid gene types
- valid_gene_types = c("lincRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene",
+ valid_gene_types = c("lincRNA", "lncRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene",
  "IG_V_gene", "TR_C_gene","TR_D_gene","TR_J_gene", "TR_V_gene",
  "3prime_overlapping_ncrna","known_ncrna", "processed_transcript",
  "antisense","sense_intronic","sense_overlapping", "leafcutter")