#!/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

tablein=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/denoise-table-merge.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/
filtdir=/data/mramseylab/proc_reads/
# filter status of input files, "initial" is the 1st pass no filter at all
# "initial-human" is the initial data but for only human samples, no mock or control samples
fil=initial-human  

#note must make directores needed BEFORE running the below command
mkdir $filtdir$fil

qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir\Serum5.tsv \
  --p-where "[Source]='Human'" \
  --o-filtered-table $filtdir$fil/$fil-table.qza