#!/bin/bash
#SBATCH -t 06:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=100g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

array=( A An S  )

for i in "${array[@]}"
do

rawdir=/data/mramseylab/raw_reads/trip"$i"
visdir=/data/mramseylab/scripts/ALScripts/triptest/visualizations_"$i"

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path $rawdir \
--input-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path $rawdir/demux-master-pseudo-"$i".qza

qiime demux summarize \
--i-data $rawdir/demux-master-pseudo-"$i".qza \
--o-visualization $visdir/demux-master-pseudo-vis"$i".qzv

done