#!/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 QIIME2/2024.2

rawdir=/data/mramseylab/raw_reads/2022_AL_SUPP/AL_2022
procdir=/data/mramseylab/16S/proc_reads/2022_AL_SUPP/2022

qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path $rawdir \
--input-format CasavaOneEightSingleLanePerSampleDirFmt \
--output-path $procdir/2022-demux-trips.qza

qiime demux summarize \
--i-data $procdir/2022-demux-trips.qza \
--o-visualization $procdir/2022-pseudo-summary.qzv