manifest.yaml

#############
# VCF FILES #
#############

# # add limit
# limit: 100

# The local file paths or URLs to vcf files to be processed
vcf_files:
  - "tests/fixtures/1kGP.chr1.1000.vcf"
  - "tests/fixtures/1kGP.chr1.1000.slim.vcf"

###############
# DIRECTORIES #
###############

# where to store output like log files and metrics files
state_directory: "state/"

# where to store input data like VCF files and a copy of the manifest used
work_directory: "work/"

# Stores the vrs_id and metakb cache if cache_enabled (defaults to cache/)
cache_directory: "cache/"

# installation path for seqrepo (reference sequences)
seqrepo_directory: "~/seqrepo/latest"

# where to find JSON evidence files
metakb_directory: "tests/fixtures/metakb"

#################
# CONFIGURATION #
#################

# Number of threads to use for processing, defaults to 2
num_threads: 2

# Control if cache is used
cache_enabled: false

# max lines from a vcf file (optional)
# limit: 30000

# normalize the VRS ids
normalize: true

# compute VRS IDs for the reference allele as well as the alt
compute_for_ref: false

# used as the max for progress bars
estimated_vcf_lines: 4000000

# whether to disable progress bars pro
disable_progress_bars: False