q2b_dada2.batch

#!/bin/bash
set -euxo pipefail
cd $(dirname `readlink -f $0`)

prefix=`cat configuration.txt | grep "^prefix" | cut -d "=" -f 2`
CPU=`cat configuration.txt | grep "^CPU" | cut -d "=" -f 2`
dada2_max_ee=`cat configuration.txt | grep "^dada2_max_ee" | cut -d "=" -f 2`
dada2_pooling_method=`cat configuration.txt | grep "^dada2_pooling_method" | cut -d "=" -f 2`
dada2_chimera_method=`cat configuration.txt | grep "^dada2_chimera_method" | cut -d "=" -f 2`
dada2_min_fold_parent_over_abundance=`cat configuration.txt | grep "^dada2_min_fold_parent_over_abundance" | cut -d "=" -f 2`




manifest="${prefix}_manifest"
prefix_dada2="${prefix}_da2"

echo "#============ This script is going to output these files ..."
echo
echo ${prefix_dada2}_init.qza
echo ${prefix_dada2}_sum.qzv
echo
echo ${prefix_dada2}_tab.qza
echo ${prefix_dada2}_tab.qzv
echo
echo ${prefix_dada2}_rep.qza
echo ${prefix_dada2}_rep.qzv
echo
echo ${prefix_dada2}_stat.qza
echo ${prefix_dada2}_stat.qzv
echo
echo "#============ running batch ..."

qiime tools import \
	--type 'SampleData[SequencesWithQuality]' \
	--input-format SingleEndFastqManifestPhred33V2 \
	--input-path  ${manifest}.tsv \
	--output-path ${prefix_dada2}_init.qza
	
qiime demux summarize \
	--i-data ${prefix_dada2}_init.qza \
	--o-visualization ${prefix_dada2}_sum.qzv

echo
echo ${prefix_dada2}_init.qza
echo ${prefix_dada2}_sum.qzv
echo "#============ finished qiime tools import ..."
echo

######## dada2
qiime dada2 denoise-single \
	--p-n-threads ${CPU} \
	--p-trunc-len 0 \
	--p-max-ee ${dada2_max_ee} \
	--p-pooling-method ${dada2_pooling_method} \
	--p-chimera-method ${dada2_chimera_method} \
	--p-min-fold-parent-over-abundance ${dada2_min_fold_parent_over_abundance} \
	--i-demultiplexed-seqs ${prefix_dada2}_init.qza \
	--o-table ${prefix_dada2}_tab.qza \
	--o-representative-sequences ${prefix_dada2}_rep.qza \
	--o-denoising-stats ${prefix_dada2}_stat.qza
	
echo
echo ${prefix_dada2}_tab.qza
echo ${prefix_dada2}_rep.qza
echo ${prefix_dada2}_stat.qza
echo "#============ finished dada2 denoise-single ..."
echo

######## feature table 
########

qiime feature-table summarize \
  --m-sample-metadata-file ${manifest}.tsv \
  --i-table ${prefix_dada2}_tab.qza \
  --o-visualization ${prefix_dada2}_tab.qzv

qiime feature-table tabulate-seqs \
  --i-data ${prefix_dada2}_rep.qza \
  --o-visualization ${prefix_dada2}_rep.qzv

qiime metadata tabulate \
  --m-input-file ${prefix_dada2}_stat.qza \
  --o-visualization ${prefix_dada2}_stat.qzv

echo
echo ${prefix_dada2}_tab.qzv
echo ${prefix_dada2}_rep.qzv
echo ${prefix_dada2}_stat.qzv
echo "#============ finished feature-table summarize/tabulate-seqs/tabulate ..."
echo

exit 0