Create Configuration File From Arguments

Usage

create_config(outdir, type = "sc_3end", ...)

Arguments

outdir

the destination directory for the configuration file

type

use an example config, available values:

"sc_3end": - config for 10x 3' end ONT reads
"SIRV": - config for the SIRV example reads

...

Configuration parameters (using dot for nested parameters)

seed: - Integer. Seed for minimap2.
threads: - Number of threads to use.
do_barcode_demultiplex: - Boolean. Specifies whether to run the barcode demultiplexing step.
do_genome_alignment: - Boolean. Specifies whether to run the genome alignment step. TRUE is recommended
do_gene_quantification: - Boolean. Specifies whether to run gene quantification using the genome alignment results. TRUE is recommended
do_isoform_identification: - Boolean. Specifies whether to run the isoform identification step. TRUE is recommended
bambu_isoform_identification: - Boolean. Whether to use Bambu for isoform identification.
multithread_isoform_identification: - Boolean. Whether to use FLAMES' new multithreaded Cpp implementation for isoform identification.
do_read_realignment: - Boolean. Specifies whether to run the read realignment step. TRUE is recommended
do_transcript_quantification: - Boolean. Specifies whether to run the transcript quantification step. TRUE is recommended
barcode_parameters.max_bc_editdistance: - Maximum edit distance for barcode matching
barcode_parameters.pattern.primer: - Primer sequence pattern
isoform_parameters.max_dist: - Maximum distance allowed when merging splicing sites
...: - Other nested parameters, using dot to indicate nested section

Value

file path to the config file created

Details

Create a list object containing the arguments supplied in a format usable for the FLAMES pipeline, and writes the object to a JSON file, which is located with the prefix 'config_' in the supplied outdir. Default values from extdata/config_sclr_nanopore_3end.json will be used for unprovided parameters.

Simple scalar parameters can be set via the ... argument using dot notation (e.g. barcode_parameters.max_bc_editdistance = 3). For complex structured parameters such as barcode_parameters.segments (which is a JSON array of objects), it is strongly recommended to call create_config(outdir) first to generate the default JSON file, then open that file in a text editor and modify the segments array directly. See the FLAMES vignette for a worked example.

Examples

# create the default configuration file
outdir <- tempdir()
config <- create_config(outdir)
#> ℹ Writing configuration to: /tmp/Rtmp4nGYdi/config_file_48196.json

# create config with custom parameters including nested ones
config <- create_config(outdir,
  threads = 16,
  barcode_parameters.max_bc_editdistance = 3,
  barcode_parameters.pattern.primer = "ATCGATCG",
  isoform_parameters.min_sup_cnt = 10,
  # use the coverage model in oarfish
  # via supplying additional CLI arguments
  additional_arguments.oarfish = c("--model-coverage")
)
#> ℹ Writing configuration to: /tmp/Rtmp4nGYdi/config_file_48196.json