just run Phoenix

#!/usr/bin/env bash
#Pipeline for running and organizing output from PHoeNIx *without having to make a sample sheet first
#Do not use this script if you need to make the sample sheet; there is a different script for that

#Make sure PHoeNIx and Kraken2 are installed on your computer, and make sure you have the Standard-08 database installed in /kraken2-master/Standard-08

#Put all reads in /kraken2-master/reads
##Each set of reads must be in a folder with the LIMS ID as the folder name
##There cannot be any other files in the reads directory besides each set of fastq files in their folders

#Output will be in output.tsv in /kraken2-master/results
##Make sure there is not already a file called output.tsv in that directory

#Working directory must be /kraken2-master

#Before starting, activate your phoenix Conda environment (conda activate phoenix)

#Edit script so paths are correct for your computer:

samplesheet=/home/mdungsmain/Janis/Programs/Kraken2/kraken2-master/samplesheet.csv
output=/home/mdungsmain/Janis/Programs/Kraken2/kraken2-master/results/output.csv
home=/home/mdungsmain/Janis/Programs/Kraken2/kraken2-master/

cd $home

#Run PHoeNIx
nextflow run phoenix/main.nf -profile docker -entry PHOENIX --kraken2db ./Standard-08 --input $samplesheet

#Organize the output 
cd results/
for dir2 in */
do 
	printf "${dir2}" >> $output
	printf "\n\n" >> $output
	cd $dir2
	cat *summaryline.tsv >> $output
	printf "\n\n" >> $output
	cat *synopsis >> $output
	printf "\n\n" >> $output
	cd ./ANI/
	cat *fastANI.txt >> $output
	printf "\n\n" >> $output
	cd ..
	cd ./AMRFinder/
	cat *all_genes.tsv >> $output
		printf "\n\n\n\n" >> $output
	cd $results
done