runFASTQC.sh

#!/bin/bash


scriptName="runFASTQC"
function printUsage () {
    cat <<EOF

Synopsis

    $scriptName [-h | --help] Directory 

        Directory:  directory location of raw fastq files that need to be processed 
	
Output directory is fastqc and will be created upon running of script in the current folder.

<<<<<<< HEAD
Example
runFASTQC.sh /work/GIF3/archive3/Purcell/021615_albacore/
JobR_condo.sh 16 fastqc.commands 
ls fastqc_* | xargs -I xx sub xx fastqc
ls fastqc_* | xargs -I xx qsub xx

Author

    Andrew Severin, Genome Informatics Facilty, Iowa State University
    severin@iastate.edu
    15 December, 2015


EOF
}


if [ $# -lt 1 ] ; then
        printUsage
        exit 0
fi

dir=$1

ls $dir/*.fastq | xargs -I xx echo "fastqc -o fastqc xx" > fastqc.commands
mkdir fastqc