main.bitia.sh

#!/usr/bin/env bash

#fastqc *.gz

bitia tools download ./small_input_files.txt

for file in *_1.fastq.gz
do
  echo $file ${file%_1.fastq.gz}_2.fastq.gz
  trim_galore --cores 8 --gzip --fastqc --max_n 2 \
      --output_dir Trimmed_Data/ \
      --paired $file ${file%_1.fastq.gz}_2.fastq.gz

done