Deinterleave entire directory of compressed .fastq.gz files and re-compress mates

deinterleave_dir.sh

#!/bin/bash 

# Uses this incredible script, deinterleave_fastq.sh, and associated comments: https://gist.github.com/nathanhaigh/3521724

# Usage: deinterleave_dir.sh indir outdir

# Deinterleave entire directory of compressed .fastq.gz files from `indir` and re-compresses mates with 
# _R1.fastq.gz and _R2.fastq.gz suffixes to `ourdir`

# Download deinterleave_fastq.sh
wget https://gist.githubusercontent.com/nathanhaigh/3521724/raw/5d4cc310d65ce798c2b030756a2b855cf55ecbcd/deinterleave_fastq.sh

# Make output directory
mkdir $2

# Deinterleave each compressed file and save to output directory
for file in $1/*
do
        echo $file
        out1=$2/$(basename ${file%.fastq.gz})_R1.fastq.gz
        out2=$2/$(basename ${file%.fastq.gz})_R2.fastq.gz
        pigz --best --processes 16 -dc $file | bash deinterleave_fastq.sh $out1 $out2 compress
done