run_split_cstacks: run_split_cstacks

In thierrygosselin/stackr: Run stacks pipeline for RADseq analysis inside R

run_split_cstacks

Description

The function that runs cstacks

Usage

run_split_cstacks(
  catalog.id = NULL,
  o = "06_ustacks_2_gstacks",
  M = "02_project_info/population.map.catalog.tsv",
  catalog.path = NULL,
  P = "06_ustacks_2_gstacks",
  n = 1,
  parallel.core = parallel::detectCores() - 1,
  max.gaps = 2,
  min.aln.len = 0.8,
  disable.gapped = FALSE,
  k.len = NULL,
  report.mmatches = FALSE
)

thierrygosselin/stackr documentation built on April 13, 2025, 10:28 a.m.