Set pipeline configurations — config<- • FLAMES

This function sets the configuration of the pipeline.

Usage

config(pipeline) <- value

# S4 method for class 'FLAMES.Pipeline'
config(pipeline) <- value

Arguments

pipeline: An pipeline of class `FLAMES.Pipeline`.
value: A list containing the configuration of the pipeline, or a path to a JSON configuration file.

Value

An pipeline of class `FLAMES.Pipeline` with the updated configuration.

Examples

pipeline <- example_pipeline(type = "BulkPipeline")
#> Writing configuration parameters to:  /tmp/RtmpdufN84/file7a181a11abf3/config_file_31256.json 
#> Configured steps: 
#> 	genome_alignment: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
# Set a new configuration
config(pipeline) <- create_config(outdir = tempdir())
#> Writing configuration parameters to:  /tmp/RtmpdufN84/config_file_31256.json