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function nextera_trim() {
     fq=${1/-1.fq.gz/}
     fq1_in=${fq}-1.fq.gz
     fq2_in=${fq}-2.fq.gz
     fq1_out=${fq}-trim-1.fq.gz
     fq2_out=${fq}-trim-2.fq.gz
     fq1_unpaired=${fq}-unpaired-1.fq.gz
     fq2_unpaired=${fq}-unpaired-2.fq.gz
     trimmomatic PE -threads 4 ${fq1_in} ${fq2_in} ${fq1_out} ${fq1_unpaired} ${fq2_out} ${fq2_unpaired} ILLUMINACLIP:/usr/local/share/trimmomatic/adapters/NexteraPE-PE.fa:2:80:10 MINLEN:45
     shasum ${fq1_in} ${fq2_in} ${fq1_out} ${fq2_out} >> shasums_out.txt
     rm ${fq1_unpaired} ${fq2_unpaired}
     fastqc ${fq1_out} ${fq2_out} &
}

# Alt. notation
function nextera_trim() {
     fq=${1/_R1_001.fastq.gz/}
     fq1_in=${fq}_R1_001.fastq.gz
     fq2_in=${fq}_R2_001.fastq.gz
     fq1_out=${fq}-trim-1.fq.gz
     fq2_out=${fq}-trim-2.fq.gz
     fq1_unpaired=${fq}-unpaired-1.fq.gz
     fq2_unpaired=${fq}-unpaired-2.fq.gz
     trimmomatic PE -threads 4 ${fq1_in} ${fq2_in} ${fq1_out} ${fq1_unpaired} ${fq2_out} ${fq2_unpaired} ILLUMINACLIP:/exports/people/andersenlab/dec211/.linuxbrew/share/trimmomatic/adapters/NexteraPE-PE.fa:2:80:10 MINLEN:45
     shasum ${fq1_in} ${fq2_in} ${fq1_out} ${fq2_out} >> shasums_out.txt
     rm ${fq1_unpaired} ${fq2_unpaired}
     fastqc ${fq1_out} ${fq2_out} &
}

for i in `ls UChicago3*1.fq.gz | grep -v 'trim'`; do
    nextera_trim ${i}
done;