config.yaml

samples:
    # sample or id to use for generating targets
    id: "00114031182M22BFF2"
    fq_path: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/20240223_20_sample/input"
modules:
    # Should snakemake do stlfr specific analyses, false if the library isn't of linked reads
    mapping: True
    # anatation and classify
    classifed: True
    
params:
    # reference 
    smk_path: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/script/blood_viromes3" 
    # tools path
    tools: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/script/blood_viromes3/tools" 
    # smk_path: "./"
    ref_viral: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/viral_refseq/viral.1.1.genomic.fna"
    ref_T2T: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/human/chm13v2.0.fa"
    ref_pangenome: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/Chinese_Pangenome/CPC.Phase1.CHM13v2-full_decoy.fa"
    # repeats region 
    repeats: "/WORK/gzfezx_shhli_3/BioDatahub/human_reference/GRCh38/LCR-hs38_rmsk.bed"
    # kraken2 database
    k2_viral: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/k2_viral_20231009"
    # blastn_db: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/nt_db/nt"
    k2_db: "/BIGDATA2/gzfezx_shhli_2/USER/luozhenyu/database/kraken2-microbial-fatfree"

threads:
    bwa: 24