workflow.yaml

# QuaC workflow config
# See src/setup_dependency_datasets.sh to download necessary datasets.

datasets:
  # path to ref genome
  ref: "data/external/dependency_datasets/reference_genome/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
  # path to Somalier dataset dependencies. Available at https://github.com/brentp/somalier
  somalier:
    sites: "data/external/dependency_datasets/somalier/sites.hg38.vcf.gz"
    labels_1kg: "data/external/dependency_datasets/somalier/ancestry-labels-1kg.tsv"
    somalier_1kg: "data/external/dependency_datasets/somalier/1kg-somalier/"
  # path to verifyBamID dataset dependencies. Available at https://github.com/Griffan/VerifyBamID
  verifyBamID:
    svd_dat_wgs: "data/external/dependency_datasets/verifyBamID/1000g.phase3.100k.b38.vcf.gz.dat"
    # retrieved from https://github.com/Griffan/VerifyBamID and 'chr' prefix added to the contigs
    svd_dat_exome: "data/external/dependency_datasets/verifyBamID/exome/1000g.phase3.10k.b38_chr.exome.vcf.gz.dat"

#### hardware resources for certain tools used in snakemake piepline ####
resources:
  qualimap_bamqc:
    no_cpu: 1 # CGDS uses 2
    mem_per_cpu: "4G" # CGDS uses 24G
  mosdepth_coverage:
    no_cpu: 1 # CGDS uses 4
  verifybamid:
    no_cpu: 1 # CGDS uses 4