Set controllers

Sets the controllers for the pipeline.

Usage

controllers(pipeline) <- value

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

Arguments

pipeline

A FLAMES.Pipeline object.

value

A crew_class_controller object or a named list of crew_class_controller objects. If a single controller is provided, it will be used for all steps in the pipeline. If a named list is provided, steps with names that match the names of the list will use the corresponding controller, and steps without a specified controller will use the current R session.

Value

An updated FLAMES.Pipeline object with the specified controllers.

Examples

pipeline <- example_pipeline()
#> Writing configuration parameters to:  /tmp/RtmpA5lNG6/file3290611574d0/config_file_12944.json 
#> Configured steps: 
#> 	barcode_demultiplex: TRUE
#> 	genome_alignment: TRUE
#> 	gene_quantification: TRUE
#> 	isoform_identification: TRUE
#> 	read_realignment: TRUE
#> 	transcript_quantification: TRUE
#> samtools not found, will use Rsamtools package instead
# Only set the genome alignment controller
controllers(pipeline) <- list(genome_alignment = crew::crew_controller_local())
# Same as above
controllers(pipeline)[["genome_alignment"]] <- crew::crew_controller_local()
# Set a controller for all steps
controllers(pipeline) <- crew::crew_controller_local()
# Unset all controllers and use the current R session
controllers(pipeline) <- list()