#!/bin/bash
# Combines the output from the ONT GridION into a single compressed fastq file

# Initiation, get some important info
RUNNAME=$(basename "${1}")
NUMCPU=$(grep -c processor < /proc/cpuinfo)
OUTNAME="$RUNNAME"_demux

#echo "$RUNNAME"
#echo "$NUMCPU"
#echo "$OUTNAME"

# Let guppy do its thing
guppy_barcoder --input_path "$RUNNAME" --save_path "$OUTNAME" --recursive --records_per_fastq 0 --compress_fastq --worker_threads "$NUMCPU" --device cuda:all:100%

# Unzip the fastqs
parallel --gnu -j12 --eta gunzip ::: "$OUTNAME"/*/*.fastq.gz

# Squish them together
cat "$OUTNAME"/*/*.fastq > "$OUTNAME"/"$RUNNAME".fastq

# Rezip the fastqs
parallel --gnu -j"$NUMCPU" --eta gzip ::: "$OUTNAME"/*/*.fastq
gzip "$OUTNAME"/"$RUNNAME".fastq