2021-02-09 12:52:44 +01:00
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#!/bin/bash
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#SBATCH --job-name=fastqc
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#SBATCH --time=0-12:00:00
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#SBATCH --ntasks=1
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#SBATCH --mem=15G
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#SBATCH --qos=regular
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set -e
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set -u
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set -x
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set -o pipefail
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module purge
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module load Java
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module load FastQC
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dir_raw_fastq="$(pwd)/fastq/raw"
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dir_fastqc="$(pwd)/fastqc"
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[ -d "${dir_fastqc}" ] || mkdir -p "${dir_fastqc}"
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# Run FastQC
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files=$(find -L "$dir_raw_fastq" -type f -iname "*.fastq.gz")
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for file in $files; do
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filename=$(basename "$file")
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fastqc -o "$dir_fastqc" "$file" &
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done
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wait
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