run.alignment.sample {varitas}

Run alignment for a single sample

Description

Run alignment for a single sample

Usage

run.alignment.sample(fastq.files, sample.id, output.directory = NULL,
  output.filename = NULL, code.directory = NULL,
  log.directory = NULL, config.file = NULL, job.dependencies = NULL,
  job.name = NULL, job.group = NULL, quiet = FALSE,
  verify.options = !quiet)

Arguments

fastq.files

Paths to FASTQ files (one file if single-end reads, two files if paired-end)

sample.id

Sample ID for labelling

output.directory

Path to output directory

output.filename

Name of resulting VCF file (defaults to SAMPLE_ID.vcf)

code.directory

Path to directory where code should be stored

log.directory

Path to directory where log files should be stored

config.file

Path to config file

job.dependencies

Vector with names of job dependencies

job.name

Name of job to be submitted

job.group

Group job should belong to

quiet

Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging.

verify.options

Logical indicating whether to run verify.varitas.options