panel-filtering spec

This repo contains a slurm-pipeline specification file (specification.json) and associated scripts for filtering BLAST results (specifically, blastx) and creating a panel.

Usage

It's assumed you've already run the pipeline on the samples you're interested in.

To add processing for a sample. Do something like this:

$ mkdir 160211-25
$ cd 160211-25
$ git clone https://github.com/akifoss/panel-fitering
$ make run

This will run panel.sh on all the blast results for sample 160211-25.

Output

The scripts in 01-panel, 02-stop, etc. are all submitted by sbatch for execution under SLURM. 01-panel leaves its output in 01-panel/out and 01-panel/summary-virus.

Cleaning up

$ make clean

Removes all intermediate files and the final output in 01-panel/out.