#!/bin/bash
#SBATCH -t 2:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL
#./import-fastq.sh

module load QIIME2/2019.7

for d in /data/mramseylab/raw_reads/2018_Serum/Run* ;
do
SUFX=${d#*Run}

qiime tools import \
  --type 'SampleData[PairedEndSequencesWithQuality]' \
  --input-path /data/mramseylab/raw_reads/2018_Serum/Run$SUFX \
  --input-format CasavaOneEightSingleLanePerSampleDirFmt \
  --output-path /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/demux-$SUFX.qza

qiime demux summarize \
  --i-data /data/mramseylab/raw_reads/2018_Serum/Run$SUFX/demux-$SUFX.qza \
  --o-visualization /data/mramseylab/visualizations/demux-$SUFX.qzv

done