Generate sample sheet for DRAGEN TSO500 Anaylsis Pipeline input based on TSO500 sample sheet.

Usage

generate_dragen_samplesheet(
  samplesheet,
  file_format_version = "2",
  run_name = "RunName",
  instrument_type = "NovaSeq",
  software_version = "3.10.9",
  adapter_read1,
  adapter_read2,
  adapter_behavior = "trim",
  patient_column = "Pat_ID",
  minimum_trimmed_read_length = 35,
  mask_short_reads = 35,
  outfile
)

Arguments

samplesheet: path to TSO500 sample sheet
file_format_version: the version of the file format (default: 2)
run_name: the run name (default: RunName)
instrument_type: path to output file
software_version: The software version (default: 3.10.9)
adapter_read1: index read1 sequence
adapter_read2: index read2 sequence
adapter_behavior: this indicates that the BCL Convert software trims the specified adapter sequences from each read (default: trim)
patient_column: column that holds the subject information (default: Pat_ID)
minimum_trimmed_read_length: reads with a length trimmed below this point are masked (default: 35)
mask_short_reads: reads with a length trimmed below this point are masked (default: 35)
outfile: path to output CSV file

Value

the dragen analysis input sample sheet