run.alignment {varitas}

Run alignment

Description

Run alignment

Usage

run.alignment(fastq.specification, output.directory, paired.end = FALSE,
  sample.directories = TRUE, output.subdirectory = FALSE,
  job.name.prefix = NULL, job.group = "alignment", quiet = FALSE,
  verify.options = !quiet)

Arguments

fastq.specification

Data frame detailing FASTQ files to be processed, typically from prepare.fastq.specification

output.directory

Path to project directory

paired.end

Logical indicating whether paired-end sequencing was performed

sample.directories

Logical indicating whether all sample files should be saved to sample-specific subdirectories (will be created)

output.subdirectory

If further nesting is required, name of subdirectory. If no further nesting, set to FALSE

job.name.prefix

Prefix for job names on the cluster

job.group

Group job should be associated with on cluster

quiet

Logical indicating whether to print commands to screen rather than submit them

verify.options

Logical indicating whether to run verify.varitas.options

Details

Runs alignment (and related processing steps) on each sample.

Value

None

Examples

run.alignment(
  fastq.specification = data.frame(
    sample.id = c('1', '2'),
    reads = c('1-R1.fastq.gz', '2-R1.fastq.gz'),
    mates = c('1-R2.fastq.gz', '2-R2.fastq.gz'),
    patient.id = c('P1', 'P1'),
    tissue = c('tumour', 'normal')
  ),
  output.directory = '.',
  quiet = TRUE,
  paired.end = TRUE
)