unicycler: Unicycler Client

View source: R/tools.R

unicyclerR Documentation

Unicycler Client

Description

Runs Unicycler via Toolchest.

Usage

unicycler(
  tool_args = "",
  read_one = NULL,
  read_two = NULL,
  long_reads = NULL,
  output_path = NULL,
  ...
)

Arguments

tool_args

(optional) Additional arguments to be passed to Unicycler.

read_one

Path of input file (FASTQ) to be passed in as Read 1 (-1).

read_two

Path of input file (FASTQ) to be passed in as Read 2 (-2).

long_reads

Path of input file (FASTA) to be passed in as long reads (-l).

output_path

(optional) Path to a directory where the output file(s) will be downloaded.

is_async

(optional) Whether to run a job asynchronously. Defaults to false.

Value

Reference to an object with output location data.

Note

If some but not all of read_one, read_two, or long_reads are unspecified, Toolchest will assume that they are intended to be blank. If all are left blank, the user will be prompted to provide input file(s) and option(s).

At least one input filepath is needed for Toolchest to run Unicycler.

If output_path is left unspecified, downloading will be skipped.


gotoolchest/toolchest-client-r documentation built on July 14, 2022, 7 a.m.