fastqscreener wrapper

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