#!/bin/bash
cd moving-pictures/

# importing data
echo 'Importing Data ...'

qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza


# check the UUID, type, and format of your newly-imported sequences
echo 'UUID, type, and format imported sequences ...'
qiime tools peek emp-single-end-sequences.qza


# Demultiplexing sequences

echo 'Demultiplexing sequences ...'

qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-column barcode-sequence \
  --o-per-sample-sequences demux.qza \
  --o-error-correction-details demux-details.qza

# generate a summary of the demultiplexing results
echo 'Generating summary ...'
qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv

# Sequence quality control and feature table construction

echo 'Sequence quality control and feature table construction ...'

qiime dada2 denoise-single \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left 0 \
  --p-trunc-len 120 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza \
  --o-denoising-stats stats-dada2.qza

qiime metadata tabulate \
  --m-input-file stats-dada2.qza \
  --o-visualization stats-dada2.qzv

echo 'Renaming outputs ...'

mv rep-seqs-dada2.qza rep-seqs.qza
mv table-dada2.qza table.qza

cd ../