Pete fastqc

fastqc.sh

#!/bin/bash
set -e
set -x

if [ $# -ne 1 ]
then
echo "USAGE: fastqc.sh SAMPLENAME"
fi

sample=$1
sample_dir=reads/$sample

fastqs="$(ls $sample_dir/*.fastq.gz)"

mkdir qc/$sample

fastqc -o qc/$sample $fastqs

in parallel:

echo -e "Sample1\nSample2" | parallel bash fastqc.sh {}

Assuming sample names of Sample1 and Sample2

or, more properly:

function findSamples () {
find reads/  -mindepth 1 -maxdepth 1 -type d -exec basename {} \;| tr ' ' '\n'
}

findSamples | parallel .....

But be careful with tr ' ' '\n', it will fuck things up if the sample names have spaces in them