#!/bin/bash
#SBATCH -t 1:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=kramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load bio/cutadapt/3.5-GCCcore-11.2.0

cd /data/kramseylab/compressed_fastq/230322_TnSeq/

echo -e "Transposon trimming results:\n" > 230404_adapttrimlog.txt

for f in *.fastq;
do
    PREFIX1="${f%.fastq}"
    
cutadapt -a ACAGGTTGGATGATAAGTCCCCGGTCTTCGTAATCTCGTATGCCGTCTTCTGCTTG --no-indels --discard-untrimmed -m 7 -o $PREFIX1\_trimmed.fastq $PREFIX1\.fastq >> 230404_adapttrimlog.txt

done