#!/bin/bash

mkdir -p atacama-tutorial
cd atacama-tutorial

wget \
  -O "sample-metadata.tsv" \
  "https://data.qiime2.org/2020.11/tutorials/atacama-soils/sample_metadata.tsv"


mkdir -p emp-paired-end-sequences

wget \
  -O "emp-paired-end-sequences/forward.fastq.gz" \
  "https://data.qiime2.org/2020.11/tutorials/atacama-soils/10p/forward.fastq.gz"

wget \
  -O "emp-paired-end-sequences/reverse.fastq.gz" \
  "https://data.qiime2.org/2020.11/tutorials/atacama-soils/10p/reverse.fastq.gz"


wget \
  -O "emp-paired-end-sequences/barcodes.fastq.gz" \
  "https://data.qiime2.org/2020.11/tutorials/atacama-soils/10p/barcodes.fastq.gz"


echo "Paired-end read analysis commands ... "

qiime tools import \
  --type EMPPairedEndSequences \
  --input-path emp-paired-end-sequences \
  --output-path emp-paired-end-sequences.qza

qiime demux emp-paired \
  --verbose \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-category BarcodeSequence \
  --i-seqs emp-paired-end-sequences.qza \
  --o-per-sample-sequences demux \
 --p-rev-comp-mapping-barcodes

qiime demux summarize \
  --verbose \
  --i-data demux.qza \
  --o-visualization demux.qzv

qiime dada2 denoise-paired \
  --verbose \
  --p-n-threads $SLURM_CPUS_PER_TASK \
  --i-demultiplexed-seqs demux.qza \
  --o-table table \
  --o-representative-sequences rep-seqs \
  --p-trim-left-f 13 \
  --p-trim-left-r 13 \
  --p-trunc-len-f 150 \
  --p-trunc-len-r 150

qiime feature-table summarize \
  --verbose \
  --i-table table.qza \
  --o-visualization table.qzv \
  --m-sample-metadata-file sample-metadata.tsv

qiime feature-table tabulate-seqs \
  --verbose \
  --i-data rep-seqs.qza \
  --o-visualization rep-seqs.qzv