run.alignment.sample: Run alignment for a single sample
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Run alignment for a single sample

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)

`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