run.all.scripts {varitas}

Run all the generated bash scripts without HPC commands

Description

Run all the scripts generated by previous parts of the pipeline, without using HPC commands

Usage

run.all.scripts(output.directory, stages.to.run = c("alignment", "qc",
  "calling", "annotation", "merging"), variant.callers = NULL,
  quiet = FALSE)

Arguments

output.directory

Main directory where all files should be saved

stages.to.run

A character vector of all stages that need running

variant.callers

A character vector of variant callers to run

quiet

Logical indicating whether to print commands to screen rather than submit jobs. Defaults to FALSE, can be useful to set to TRUE for testing.

Value

None