Where was this used:

• Ecoli paper (add link to paper)
• Staph pseudo paper (add link to paper)

What is this pipeline used for:

This pipeline is very versatile - it can be used for anything from annotating prokaryotic genomes, to pangenome analyses, to identifying genes associated with a particular phenotype (AMR, diagnostic, etc), and beyond.

Steps of the pipeline:

1. download/ retrieve data — this can be raw data to assemble, or assemblies
2. Assemble genomes (if not already done) — SKESA documentation here —> https://github.com/ncbi/SKESA
3. QC assemblies —
4. Annotate data — prokka documentation here —> https://github.com/tseemann/prokka
   1. example code for Salmonella dublin genome annotation.

#!/bin/bash

#Created 07/01/2024 by: Jordan Zehr and Gayatri Anil

## invoke prokka, according to biohpc documentation ##
export PROKKA_CMD="singularity run -C -B $PWD --pwd $PWD /programs/prokka-1.14.5-r9/prokka.sif"

## in a directory that contains assembles, loop over all fna files ##
for file in ls salDubgenomes-test/GCA*.fna; do
	
	
	#take the filename string and grab FROM character 19 to the end, 
	#then in that string get me the first 15 characters.
	#This will be the GCA... which we will use later to set the output directory
	
	
	
	## print out which GCA you are running on ## 
	echo "RUNNING PROKKA ON --> $acc"
	
	## do a check to see if the output directory already exists ## 
	if [ -d prokka-dublin-results/${acc} ]; then 
		
		## if it does, print out that its already done and include the GCA ##
		echo "ALREADY DONE with -- $acc"
		
	## otherwise ##	
	else
		
		#run prokka! 
		#--outdir - set the output directory
		#--force - force it to make that dir, and use the GCA to create the dir
		#--prefix - determines what to call the output dir
		#$file - which GCA.fna prokka will run on.
		
		$PROKKA_CMD prokka --outdir prokka-dublin-results/${acc} --force --prefix ${acc} $file 
	fi
done