search

artic-network / rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time
GNU General Public License v3.0
79 stars 34 forks source link

Improve documentation of config args to post processing scripts #55

Open aineniamh opened 4 years ago

aineniamh commented 4 years ago

To allow binlorry to easily bin_by sample name, we need a column with that information, in addition to the barcode information already provided.

This only comes into play when you want to run multiple analyses at a time as currently the binlorry call uses the --filter_by flag and we sub in barcode and sample names at that point.

jameshadfield commented 4 years ago

This information can (should) be provided by triggerPostProcessing to any downstream analysis tool such as binlorry. But it can't be stored in the annotation csv as RAMPART allows you to dynamically change the barcode - sample mapping via the UI (click the "config" icon).

jameshadfield commented 4 years ago

As of 1.1.0 this info is passed to binlorry via the snakemake config args sample_name=Kikwit barcodes=NB03 samples="{Kikwit: [NB03]}". Note that the UI can currently can only trigger them one sample at a time. Leaving this open as it needs documentation.