run.post.processing {varitas}

run.post.processing

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
)