This commit is contained in:
kuoi 2024-06-05 15:53:49 +10:00
commit d639d38659

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batch.sh Normal file
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### Environment Setting
DirRaw=00_raw
DirQcTrim=01_fastp
DirAssembly=02_spades
### Get some arrays
cd $DirRaw
readarray -t full_names < <(ls | awk -F '_' '{print $1 "_" $2 "_" $3 "_" $4}' | uniq)
readarray -t species_names < <(ls | awk -F '_' '{print $2 "_" $3}' | uniq)
readarray -t output_names < <(ls | awk -F '_' '{print $2 "_" $3 "_" $4}' | uniq)
cd ..
length_fn=${#full_names[@]}
length_sn=${#species_names[@]}
length_on=${#output_names[@]}
### Check the arrays
if [ $length_fn -ne $length_sn ] || [ $length_fn -ne $length_on ] || [ $length_sn -ne $length_on ]
then
echo "Please check the amount number of arrays"
exit 0
fi
### Quality control && Trimming
mkdir -p $DirQcTrim
for (( i=0; i<$length_fn; i++ )); do
fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j ${species_names[$i]}.json -h ${species_names[$i]}.html -o $DirQcTrim/${output_names[$i]}_R1.fastq.gz -O $DirQcTrim/${output_names[$i]}_R2.fastq.gz -w 4
done
### De novo assembly
mkdir -p $DirAssembly
for (( i=0; i<$length_fn; i++ )); do
mkdir -p $DirAssembly/${species_names[$i]}
spades.py --pe1-1 $DirQcTrim/${output_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${output_names[$i]}_R2.fastq.gz -t 8 -k 97,107,117,127 -m 14 --careful --phred-offset 33 -o $DirAssembly/${species_names[$i]}
done