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#!/bin/bash
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R1="sample1_R1.fastq.gz"
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R2="sample1_R2.fastq.gz"
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PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
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FASTQC_OUT="${PROJECT_DIRECTORY}/step1/"
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mkdir -p "${FASTQC_OUT}"
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# Run FastQC on paired-end data.
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fastqc \
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-o "${FASTQC_OUT}" \
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"${R1}" "${R2}"
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