#!/bin/bash
qiime tools import \
--type 'SampleData[SequencesWithQuality]' \
--input-path <manifest> \
--output-path <qiime2_work_dir>/demux-single-end.qza \
--input-format SingleEndFastqManifestPhred33V2
qiime dada2 denoise-single \
--i-demultiplexed-seqs <qiime2_work_dir>/demux-single-end.qza \
--p-trunc-len 0 \
--p-n-threads 0 \
--o-representative-sequences <qiime2_work_dir>/rep-seqs.qza \
--o-table <qiime2_work_dir>/feature-table.qza \
--o-denoising-stats <qiime2_work_dir>/stats.qza

qiime feature-classifier classify-sklearn \
--i-classifier <classifier> \
--i-reads <qiime2_work_dir>/rep-seqs.qza \
--p-n-jobs 4 \
--o-classification <qiime2_work_dir>/taxonomy.qza

qiime tools export \
--input-path  <qiime2_work_dir>/feature-table.qza \
--output-path  <qiime2_work_dir>

qiime tools export \
--input-path  <qiime2_work_dir>/rep-seqs.qza \
--output-path  <qiime2_work_dir>/

qiime tools export \
--input-path  <qiime2_work_dir>/taxonomy.qza \
--output-path  <qiime2_work_dir>/


biom convert --to-tsv -i <qiime2_work_dir>/feature-table.biom -o <qiime2_work_dir>/feature-table.tsv