sc2-guide-InSilicoSCR/config.yml at master · czbiohub-sf/sc2-guide-InSilicoSCR · GitHub

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admins: chunyu.zhao@czbiohub.org

project_dir: /mnt/chunyu_6TB/cas13/20200805_sc2_guides
guide_fasta: "/mnt/chunyu_6TB/cas13/20200805_sc2_guides/guides.fa"


krakenuniq:
    viral_neighbors_db: /mnt/chunyu_6TB/cas13/dbs/viral-neighbors-20200605-wo
    refseq_bacteria_db: /mnt/chunyu_6TB/cas13/dbs/refseq-bacteria-20200607
    pathogen_db: /mnt/chunyu_6TB/cas13/dbs/pathogen-bacteria


qc:
    host_ref: /mnt/chunyu_6TB/cas13/dbs/hg38.fa
    sc2_ref: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/sc2-msspe-data/MN908947.3.fa
    threads: 8

jf:
    threads: 8

msspe:
    data_dir: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1
    samplelist_fp: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/samples.tsv
    # primer related
    fwd_primer_bedfile: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/sc2-msspe-data/SARS-COV-2_spikePrimers.bed
    fwd_primer_fasta: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/sc2-msspe-data/SARS-COV-2_spikePrimers.fasta
    xprimer_fasta: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/sc2-msspe-data/x_5_fwd_primers.fasta
    rc_primer_x_fasta: /mnt/chunyu_6TB/cas13/data/czb_msspe_run1/sc2-msspe-data/rc_primers_x_3.fasta


hmp1:
    data_dir: /mnt/chunyu_6TB/cas13/data/hmp1
    metadata_fp: /mnt/chunyu_6TB/cas13/data/hmp1/HMASM-subset-nasal.csv
    samplelist_fp: /mnt/chunyu_6TB/cas13/data/hmp1/samples.tsv