#!/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 QIIME2/2019.7

tablein=/data/mramseylab/raw_reads/AL_2023/master-denoise-table-v1v2-paired.qza
metadir=/data/mramseylab/metadata/plaque_meta_6.tsv
filtdir=/data/mramseylab/proc_reads/2023_Master
rawdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2
fil=/FilteredSamples

mkdir $filtdir$fil


qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[variable-type] = ('experimental')" \
  --o-filtered-table  $filtdir/master-denoise-table.qza

qiime feature-table summarize \
  --i-table $filtdir/master-denoise-table.qza \
  --o-visualization $filtdir$fil/filter.qzv \
  --m-sample-metadata-file $metadir \

qiime feature-table filter-features \
      --i-table $filtdir/master-denoise-table.qza \
      --p-min-frequency 5 \
      --o-filtered-table $filtdir$fil/master-denoise-filtered-5.qza
    
    #Making visualization at each step to monitor loss of taxa numbers
    qiime feature-table summarize \
      --i-table $filtdir$fil/master-denoise-filtered-5.qza \
      --o-visualization $filtdir$fil/filter_feq_5.qzv \
      --m-sample-metadata-file $metadir \
    
    #filter for features present in more than 2 libraries
    qiime feature-table filter-features \
      --i-table $filtdir$fil/master-denoise-filtered-5.qza \
      --p-min-samples 2 \
      --o-filtered-table $filtdir$fil/filter_feat_2_feq_5.qza
    
    qiime feature-table summarize \
      --i-table $filtdir$fil/filter_feat_2_feq_5.qza \
      --o-visualization $filtdir$fil/filter_feat_2_feq_5.qzv \
      --m-sample-metadata-file $metadir \
    
    #Filter things with less than 20 reads per sample
    qiime feature-table filter-samples \
      --i-table $filtdir$fil/MinFil-table_NC_AL.qza \
      --p-min-frequency 10 \
      --o-filtered-table $filtdir$fil/MinFil_20_AL.qza
    
    qiime feature-table summarize \
      --i-table $filtdir$fil/filter_feat_2_feq_10.qza  \
      --o-visualization $filtdir$fil/filter_feat_2_feq_10.qzv  \
      --m-sample-metadata-file $metadir \