search

mritchielab / FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.
https://mritchielab.github.io/FLAMES/
GNU General Public License v3.0
14 stars 9 forks source link

Defining custom parameters in the config file #43

Open vsuppiyar opened 2 weeks ago

vsuppiyar commented 2 weeks ago

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 commented 2 weeks ago

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 commented 2 weeks ago

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