Defining custom parameters in the config file

[vsuppiyar]

Specifying in this step UMI, polyT, and TSO_seq :

config_file <- FLAMES::create_config(outdir, type = "SIRV", do_barcode_demultiplex = TRUE)

doesn't seem to be properly working. I observed this behaviour particularly for setting the UMI and polyT.

The default values are still present in the config file after setting them and do not seem to be overwritten by the custom values.

[ChangqingW]

There is a problem with how that function handles nested parameters. For now you can specify it as
create_config('/tmp', pattern=list(UMI="test1", BC = "test2"))

[ChangqingW]

I'll probably just move pattern out from barcode_parameters to avoid the extra nesting in the next release.