config.yaml 617 Bytes
Newer Older
1
2
3
4
5
6
7
8
## directories ##

working_dir: "temp/"

results_dir: "results/"

data_dir: "../data/"

WJH58's avatar
WJH58 committed
9
units : "units.tsv"
10
11
12
13
14
15
16
17

## genome reference ##

genome_fasta_url : "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz"



## trimmomatic ##
WJH58's avatar
WJH58 committed
18
19
20
21
22
23
24
25
26
27
28
trimmomatic:
  adapters:               "adapters.fasta"
  seedMisMatches:         '2'
  palindromeClipTreshold: '30'
  simpleClipThreshold:    '10'
  LeadMinTrimQual:        '3'
  TrailMinTrimQual:       '3'
  windowSize:             '4'
  avgMinQual:             '15'
  minReadLength:          '40'
  phred:                  '-phred33'