config.yaml

## Configure variables for subsampling workflow.
## See dag.svg for possible target output files.

# Target subsampling schemes as output folders.
folders:
  ["sub", "sub_random", 
  "sub_rtl", "sub_uniform-tempo", 
  "sub_uniform-spatiotempo",
  "sub_uniform-spatiotempo-alt",
  "sub_postsubsampling"]

# Target output file types per subsampling scheme.
types:
  ["fasttre.nwk.png", "rtt.png"]

# Prefix of input sample or clade. 
sample:
  gisaid_cov_mafft

# No. of sequences to sample for simple random sampling scheme.
randsize:
  200

# Retained relative tree length for RTL subsampling scheme.
rtl:
  0.75

# Threads to use for RTL subsampling scheme. 
rtl_threads:
  4

# No. of sequences to sample for the 2 uniform schemes.
unisize:
  200

# No. of time intervals to sample from in the 2 uniform schemes.
uniinterv:
  16

# % of sequences to sample per deme under postsubsampling scheme.
fixperc:
  0.25

# Max no. of sequences from each deme to sample at random.
balanced_randsize:
  34