#!/usr/bin/env bash

FILES=$(cat ./data/SampleInputFileLinks.txt)
for file in $FILES; do
    # --no-clobber, do not download if file already exists.
    wget -nc $file
done

fastqc *fastq.gz
trim_galore --gzip --fastqc --max_n 2 --paired --length 50 \
     SRR11862696_1.fastq.gz SRR11862696_2.fastq.gz