64 lines
1.7 KiB
Bash
64 lines
1.7 KiB
Bash
#!/bin/bash
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#SBATCH --job-name=trimming
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#SBATCH --time=2-00:00:00
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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 TrimGalore
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dir_raw_fastq="$(pwd)/fastq/raw"
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dir_trimmed_fastq="$(pwd)/fastq/trimmed"
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dir_trimmed_fastq_reports="$(pwd)/fastq/trimmed/reports"
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adapter_3p="TGGAATTCTCGG" # is _R1
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adapter_5p="GATCGTCGGACT" # is _R2
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[ -d "${dir_trimmed_fastq_reports}" ] || mkdir -p "${dir_trimmed_fastq_reports}"
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# Trim all adapters from the sequences
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while IFS=, read -r GSID Sample
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do
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echo ">> Executing trimming of $GSID (${#GSID})"
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if [ "${#GSID}" == "18" ]; then # check length - don't include sample pools
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for fqFile in $(find -L "$dir_raw_fastq" -maxdepth 1 -type f -iname "*${GSID}*.fastq.gz"); do
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newFilename=${fqFile/.fastq.gz/_trimmed.fq.gz}
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if [ -f "${newFilename}" ]; then
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echo ">>File exists ${newFilename}. Skipping"
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else
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echo ">>File: ${fqFile}"
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if grep -q "_R1" <<< $(basename "$fqFile"); then
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adapter_seq=$adapter_3p
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elif grep -q "_R2" <<< $(basename "$fqFile"); then
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adapter_seq=$adapter_5p
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fi
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echo ">>Trimming with sequence ${adapter_seq}"
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trim_galore \
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--adapter "$adapter_seq" \
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--length $(printf "$adapter_seq" | wc -m) \
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--output_dir "${dir_trimmed_fastq}" \
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--fastqc_args "--noextract" \
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"${fqFile}" &
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fi
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done
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else
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echo "Skipped."
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fi
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done < samples.csv
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wait
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mv ${dir_trimmed_fastq}/*.zip "${dir_trimmed_fastq_reports}"
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mv ${dir_trimmed_fastq}/*.txt "${dir_trimmed_fastq_reports}"
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mv ${dir_trimmed_fastq}/*.html "${dir_trimmed_fastq_reports}" |