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MADscientist314/fastqscreener.sh

Created April 28, 2021 20:02
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fastqscreener wrapper
Raw
fastqscreener.sh
threads=48
for n in $(cat manifest_02);
do
nohup fastq_screen
time
fastq_screen \
--nohits \
--threads $threads \
--subset 0 \
--outdir screened/ \
--conf fastq_screen.tmp.conf \
trimmed/$n"_1_sequence_kneaddata.trimmed.1.fastq.gz
echo "$n complete";
rm -v screened/$n"_1_sequence_kneaddata.trimmed.1.tagged.fastq.gz" > $n.fastqscreen.log;
done
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