run.post.processing: run.post.processing

In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description

Submit post-processing job to the cluster with appropriate job dependencies

Usage

run.post.processing(variant.specification, output.directory,
  code.directory = NULL, log.directory = NULL, config.file = NULL,
  job.name.prefix = NULL, quiet = FALSE, email = NULL,
  verify.options = !quiet)

Arguments

variant.specification	Data frame specifying files to be processed
output.directory	Path to directory where output should be saved
code.directory	Directory where code should be saved
log.directory	Directory where log files should be saved
config.file	Path to config file
job.name.prefix	Prefix for job names on the cluster
quiet	Logical indicating whether to print commands to screen rather than submit the job
email	Email address that should be notified when job finishes. If NULL or FALSE, no email is sent
verify.options	Logical indicating whether verify.varitas.options() should be run.

Value

None

Examples

run.post.processing(
  variant.specification = data.frame(
    sample.id = c('a', 'b'),
    vcf = c('a.vcf', 'b.vcf'),
    caller = c('mutect', 'mutect'),
    job.dependency = c('example1', 'example2')
  ),
  output.directory = '.',
  quiet = TRUE
)

varitas documentation built on Nov. 14, 2020, 1:07 a.m.