ref.yaml

#REF.yaml - File to contain paths to static reference files that RNA-Seq requires
#           for its analysis.
# NOTE: these are already pre-filled for hg38 
# NOTE: organized by assemblies
# 
# !VERY IMPORTANT: you can OVERRIDE any of these values in config.yaml!

hg38:
###annotation path 
  fasta_path: ./ref_files/fasta_reference/hg38/GRCh38.d1.vd1.CIDC.fa
  gtf_path: ./ref_files/annotations/v27/gencode.v27.annotation.gtf
  bed_path: ./ref_files/annotations/bed/refseqGenes.bed
  driver_bed_path: ./ref_files/annotations/bed/driverGene_refseqGenes.bed
  housekeeping_bed_path: ./ref_files/annotations/bed/housekeeping_refseqGenes.bed
  trust4_reper_path: ./ref_files/tools/TRUST4/hg38_bcrtcr.fa
  trust4_IMGT_path: ./ref_files/tools/TRUST4/human_IMGT+C.fa
  gmt_path: ./ref_files/static/ssgsea/c2.cp.kegg.v6.1.symbols.gmt

###index path
  star_index: ./ref_files/star_index/hg38/v27/
  star_fusion_index: ./ref_files/fusion_index/v27/ctat_genome_lib_build_dir
  salmon_index:  ./ref_files/fasta_reference/v27/new.v27.transcripts.fa
  msisensor_index: ./ref_files/msisensor2_index/hg38/microsatellite.list
  centrifuge_index: ./ref_files/centrifuge_index/p_compressed+h+v
  neoantigen_iedb_mhcI: ./ref_files/

###tool path
  msisensor2_path: ./ref_files/tools/msisensor2
  trust4_path: ./ref_files/tools/TRUST4
  arcasHLA_path: ./ref_files/tools/arcasHLA
  prada_path: ./ref_files/toolspyPRADA/pyPRADA_1.2