cutadapt_script.sh

# Specify data:
data_type=$1 # the first terminal argument will be taken as data type (single or merged)
if [[ $data_type == "single" ]] # if single ended data
then
  dataset="Raw_data/*.fastq.gz"
elif [[ $data_type == "merged" ]] # if merged data
then
  dataset=""Merged_data/*.merged.fq.gz""
fi

# Specify primer file:
primers=$2 # the second terminal argument will be taken as primer file path

# Trim primers and create a file for each locus:
trim_primers ()
{
  for file in $2
  do
    sample=$(basename -s .fastq.gz "$file")
    cutadapt -j 0 --discard-untrimmed -e 0.1 --no-indels --error-rate 0.1 -a file:$1 -o Filtered_data/{name}_$sample.fastq.gz $file
  done
}

trim_primers $primers "$dataset" | tee cutadapt_log.out