unzip_then_gzip.pbs

#!/bin/bash
#PBS -q default
#PBS -l select=1:ncpus=2:mem=250GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke

cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/rawdata

bzip2 -dkc LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R1.fastq.bz2 | gzip > ../LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R1.fastq.gz &
bzip2 -dkc LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R2.fastq.bz2 | gzip > ../LAID_OmniC_NA_NA_TTCCAAGG_Sunflower_Hetero_Red-Sunflower_OmniC_I1381_L1_R2.fastq.gz &

#wait for background processes to run
wait