guide-counter hosted with the Latch SDK
This is an implementation of the guide-counter NGS count generation tool with Latch SDK.
guide-counter is a tool for processing FASTQ files from CRISPR screen experiments to generate a matrix of per-sample guide counts. It can be used as a faster, more accurate, drop in replacement for mageck count. By default guide-counter will look for guide seqeunces in the reads with 0 or 1 mismatches vs. the expected guides, but can be run in exact matching mode.
Uploading your own guide-counter
The contents of this repository were modified from the boilerplate provided by
latch init.
You can create your own workflow by
You can replicate the contents of this repo by installing latch and creating some boilerplate like so:
$ pip install latch
$ latch init wf-guide_counter
$ cd wf-guide_counter
You will notice the structure of your boilerplate repository is roughly the same
as this repository. Just modify the code in the wf/__init__.py and the
Dockerfile, run latch register and you should be able to upload your own
version of guide-counter.