config.yaml

params:
    fastp:
      min_len : 70 # Recommended value >= 30
      adapter_r1: "AAGTCGGAGGCCAAGCGGTCTTAGGAAGACAA" #BGI-SEQ
      adapter_r2: "AAGTCGGATCGTAGCCATGTCGTTCTGTGAGCCAAGGAGTTG" #BGI-SEQ
    rmhost:
      bowtie2_index: "/path/database/humanhostbowtie2_index/chm13v2"
      threads: 2
    metaphlan4:
      do: True
      bowtie2db: "/path/database/metaphlan/metaphlan_databases"
      index: "mpa_vOct22_CHOCOPhlAnSGB_202212"
      threads: 2
    kraken2:
      do: False
      db: "/path/database/kraken_pub/k2_standard_20210517"
      confidence: 0
      threads: 2
    bracken:
      reads_len: 100
      level: ["S"]    #["D", "P", "C", "O", "F", "G", "S"]

assay:
    trimming: "1.assay/01.trimming"
    rmhost: "1.assay/02.rmhost"
    profile: 
        metaphlan4: "1.assay/03.profile/metaphlan4"
        kraken2: "1.assay/03.profile/kraken2"

results:
    "2.result"

logs:
    trimming: "1.assay/logs/01.trimming"
    rmhost: "1.assay/logs/02.rmhost"
    profile: "1.assay/logs/03.profile"

benchmarks:
    filter: "1.assay/benchmarks/01.filter"
    profile: "1.assay/benchmarks/02.profile"