#!/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, "MockQC" is just for the reads from the mock libraries
fil=MockQC

#note must make output directores needed BEFORE running the below command

qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir\Serum4.tsv \
  --p-where "[Source]='Mock'" \
  --o-filtered-table $filtdir$fil/$fil-table.qza

#note this portion overwrites the input it takes from the above command
#Using the modified silva taxonomy that we added A.baumanii to for consistency
qiime feature-table filter-features \
  --i-table $filtdir$fil/$fil-table.qza \
  --m-metadata-file $clsdir\silva-mod-taxonomy.qza \
  --o-filtered-table $filtdir$fil/$fil-table.qza

#outputs mock libraries with barplots and taxa assignments
qiime taxa barplot \
  --i-table $filtdir$fil/$fil-table.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy.qza \
  --m-metadata-file $metadir\Serum4.tsv \
  --o-visualization $filtdir$fil/$fil-bar-plots.qzv