#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7
rawdir=/data/mramseylab/raw_reads/AL_v1v2_test/
visdir=/data/mramseylab/visualizations/

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path $rawdir \
--input-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path $rawdir/demux-v1v2.qza

qiime demux summarize \
--i-data $rawdir/demux-v1v2.qza \
--o-visualization $visdir/AL_demux-v1v2.qzv