#!/bin/bash
R1="sample1_R1.fastq.gz"
R2="sample1_R2.fastq.gz"

PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
FASTQC_OUT="${PROJECT_DIRECTORY}/step1/"
mkdir -p "${FASTQC_OUT}"

# Run FastQC on paired-end data.
fastqc \
    -o "${FASTQC_OUT}" \
    "${R1}" "${R2}"