#!/bin/bash
#SBATCH -t 4:00:00
#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

module load QIIME2/2019.7

procdir=/data/mramseylab/proc_reads/
outdir=/data/mramseylab/Rexport

array=( minF AF SF NP )

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

qiime tools export \
  --input-path $procdir$i\-hum/$i\-hum-table.qza \
  --output-path $outdir/$i\-hum-table.biom

biom convert -i $outdir/$i\-hum-table.biom/feature-table.biom -o $outdir/$i\-hum-features.tsv --to-tsv

done