BUpicrust/picrust.qsub at master · Boston-University-Microbiome-Initiative/BUpicrust · GitHub

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#!/bin/bash -l
# USAGE: qsub -P <BU PROJECT NAME> picrust.qsub <ASV-TABLE.qza> <REP-SEQUENCES.qza> <OUTPUT DIRECTORY>

#$ -j y
#$ -pe omp 28

# Load parameters
PARAMETERS=$1

echo "### PICRUST ###"
cat $PARAMETERS

if [ -d $INTERDIR ]
then
    rm -rf $INTERDIR
fi

source $PARAMETERS
conda activate $CONDA_ENV

INTERDIR=$OUTDIR/intermediate/picrust

# Run picrust
cmd="qiime picrust2 full-pipeline \
    --i-table $BIOMFILE \
    --i-seq $SEQSFILE \
    --output-dir $INTERDIR \
    --p-threads $(nproc --all) \
    --p-hsp-method $HSP \
    --p-max-nsti $NSTI \
    --verbose"

echo $cmd
eval $cmd

# Extract Enzyme Classification, KEGG, and Pathway abundances
for f in ec_metagenome.qza  ko_metagenome.qza  pathway_abundance.qza
do
    qiime tools export --input-path $INTERDIR/$f --output-path $INTERDIR
    # Convert to tsv
    biom convert -i $INTERDIR/feature-table.biom -o $INTERDIR/feature-table.tsv --to-tsv
    # Move to output directory and remove stupid header
    outpath=$OUTDIR/${f%.qza}.tsv
    sed '1d' $INTERDIR/feature-table.tsv > $outpath
    echo "SAVED $outpath"
done

## Extract pathway abundances
#qiime tools export --input-path $INTERDIR/pathway_abundance.qza --output-path $INTERDIR
## Convert to tsv
#biom convert -i $INTERDIR/feature-table.biom -o $INTERDIR/feature-table.tsv --to-tsv
## Move to output directory and remove stupid header
#outpath=$OUTDIR/pathway_abundance.tsv
#sed '1d' $INTERDIR/feature-table.tsv > $outpath
#echo "SAVED $outpath"