pe-trim.sh

#!/bin/bash
#
# pe-trim.sh
# CHTC initial fastqc, trimming, and post-fastqc for paired end reads
# Usage: pe-trim.sh <samplename> <R1-fastq> <R2-fastq>

# mkdir
export HOME=$PWD
mkdir -p input output/initial_QC output/trimmed

# assign samplename to $1
# assign fastq1 to $2 and fastq2 to $3
samplename=$1
fastq1=$2
fastq2=$3

# copy reads1 and reads2 from staging to input directory
cp -r /staging/groups/roopra_group/jespina/$fastq1 input
cp -r /staging/groups/roopra_group/jespina/$fastq2 input

# print fastq filename
echo $fastq1 " and " $fastq2
echo "Running initial fastQC on " $samplename " (paired-end)"

# run initial fastqc
fastqc input/$fastq1 input/$fastq2 -o output/initial_QC 
multiqc -o output/initial_QC output/initial_QC

# trim illumina adapters
echo "Trimming " $samplename
trim_galore --paired --illumina --fastqc --cores 4 -o output/trimmed input/$fastq1 input/$fastq2  
multiqc -o output/trimmed output/trimmed

# change filenames of trimmed fq files
cd output/trimmed
r1=`basename *_val_1.fq.gz _val_1.fq.gz`
r2=`basename *_val_2.fq.gz _val_2.fq.gz`
mv *_val_1.fq.gz ${r1}_trimmed.fq.gz
mv *_val_2.fq.gz ${r2}_trimmed.fq.gz
cd ~

# tar trimmed.fq files and move to staging for alignment
tar -czvf ${samplename}_trimmed_fq.tar.gz output/trimmed/${r1}_trimmed.fq.gz output/trimmed/${r2}_trimmed.fq.gz
mv ${samplename}_trimmed_fq.tar.gz /staging/groups/roopra_group/jespina

# remove trimmed.fq.gz files before taring output folder
rm output/trimmed/${r1}_trimmed.fq.gz output/trimmed/${r2}_trimmed.fq.gz

# tar output and move to staging
tar -czvf ${samplename}_trimmed.tar.gz output/
mv ${samplename}_trimmed.tar.gz /staging/groups/roopra_group/jespina

# before script exits, remove files from working directory
rm -r input output

###END