config.yaml

params:
  reads_format: "fastq"
  reads_layout: "pe"
  samples: "samples.tsv.test"
  src: "/hwfssz1/ST_META/F16ZQSB1SY2760_PGM_ZHZ/Users/renhuahui/Virus/snakemake/src/"                                          

  trimming:
    fastp:
        do: True
        threads: 4
        disable_adapter_trimming: True
        use_slide_window: True
        compression: 6
        cut_front_window_size: 4
        cut_front_mean_quality: 20
        cut_tail_window_size: 4
        cut_tail_mean_quality: 20
        cut_right_window_size: 4
        cut_right_mean_quality: 20
        length_required: 51
        n_base_limit: 5

  report:
    seqkit:
        do: True
        threads: 4
        fq_encoding: "sanger"

  rmrRna:
    database: "/hwfssz5/ST_MCHRI/REPRO/PROJECT/P18Z10200N0183/xingyanru/Database/Individuality_ref/rRNA/SoapIndex/Human_rRNA_NCBI.fa.index"
    database2: "/hwfssz5/ST_MCHRI/REPRO/PROJECT/P18Z10200N0183/xingyanru/Database/USCS/hg19/genome/HisatIndex/hg19"
    database3: "/hwfssz5/ST_MCHRI/REPRO/PROJECT/P18Z10200N0183/xingyanru/Database/USCS/hg38/HisatIndex/hg38"
    threads: 4

  kraken2:
    # database: "/hwfssz5/ST_INFECTION/AntibioticResistance/P18Z10200N0164_Resistance_PN/PMseq/User/liangtianzhu/sortware/karken2/kraken2-2.0.8-beta/db/minikraken2/minikraken2_v1_8GB"
    database: "/ldfssz1/ST_INFECTION/2019-nCoV/liangtianzhu/Braken/braken/kraken2_db_v2/minikraken2_v2_8GB_201904_UPDATE"
    threads: 4

  bracken:
    # database: "/hwfssz5/ST_INFECTION/AntibioticResistance/P18Z10200N0164_Resistance_PN/PMseq/User/liangtianzhu/sortware/karken2/kraken2-2.0.8-beta/db/minikraken2/minikraken2_v1_8GB"
    database: "/ldfssz1/ST_INFECTION/2019-nCoV/liangtianzhu/Braken/braken/kraken2_db_v2/minikraken2_v2_8GB_201904_UPDATE"
    threshold: 10

  rmkrahost:
    threads: 4

  sortmerna:
    threads: 4
    ref: "--ref /ldfssz1/ST_META/share/User/zhujiahui/software/sortmerna-4.2.0-Linux/database/silva-bac-16s-id90.fasta --ref /ldfssz1/ST_META/share/User/zhujiahui/software/sortmerna-4.2.0-Linux/database/silva-bac-23s-id98.fasta --ref /ldfssz1/ST_META/share/User/zhujiahui/software/sortmerna-4.2.0-Linux/database/rfam-5s-database-id98.fasta"
    options: "--fastx --paired_in --out2"

  metaphlan2:
    threads: 4

  kraken2x:
    database: "/hwfssz1/ST_META/F16ZQSB1SY2760_PGM_ZHZ/BC_TMP/nCov-test/refseq/kraken2/refseq_pro"
    threads: 4

results:
    trimming: "results/01.trimming"
    report:
        base_dir: "results/03.report"
        trimming: "results/03.report/01.trimming"
    rmrRna: "results/02.rmrRna"
    kraken2: "results/03.kraken2"
    bracken: "results/03.kraken2/bracken"
    rmhost: "results/04.rmkrahost"
    sortmerna: "results/05.sortmerna"
    kraken2x: "results/06.kraken2x"
    metaphlan2: "results/07.metaphlan2"

logs:
    trimming: assay/01.trimming/logs
    rmrRna: assay/02.rmrRna/logs
    kraken2: assay/03.kraken2/logs
    bracken: assay/03.kraken2/bracken/logs
    rmkrahost: assay/04.kraken2/rmkrahost/logs
    kraken2x: assay/06.kraken2x/logs