#config file used to map bisulphite seq data. Conver to .yaml format if using with pipeline
THREADS: 4
FILTER:
  # adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
  # extra_params_trim:  ' -a "AAAAAAA -a TTTTTTT " --clip_R2 10 --clip_R1 10 --phred33 --length 20 '
  extra_params_trim:  " -a T{20} -a2 A{20} --phred33 --length 20 "
  # example for trimming 10bp off 5'
  # extra_params_trim: --clip_R2 10 --clip_R1 10

MAPPING:
  # this folder must contain the bismark index, i.e. a folder "Bisulfite_Genome" 
  # along with the fa file it was build from (e.g. chloroplast.fa)
  reference: "/data/public_data/tomato/S_lycopersicum/plusChloroplast/"
  # used as short version to name output filnames for mapping
  # this should ideally be the filename (e.g. chloroplast.fa) without .fa extension
  reference_short: "S_lycopersicum_chromosomes.3.00_plusChloroplast"
  extra_params_bismark: " --dovetail --score_min L,0,-0.4 -un"
  # example to relax mapping
  # extra_params_bismark: " --score_min L,0,-0.4 --un"

REPORT:
  binsize:  50
  extra_params_bamCoverage: ""
  extra_params_meth_extractor:  " --comprehensive --report --buffer_size 8G"
  extra_params_bismark2bedGraph: ""
  extra_params_coverage2cytosine: " --CX"