Remove primers from paired end reads using Cutadapt and SeqFu

cutadapt-primers.sh

#!/bin/bash
set -euo pipefail

FOR=CCTACGGGNGGCWGCAG
REV=GGACTACHVGGGTATCTAATCC

# Cutadapt options
MINL=250
EXTRA=" --report minimal  --cores 0 --discard-untrimmed  "

# Compute RC
FORRC=$(seqfu rc $FOR)
REVRC=$(seqfu rc $REV)

# CHECK
CUTADAPT=$(cutadapt --version)
SEQFU=$(seqfu | grep version | cut -f 2 -d :)

# Print versions
echo CUTADAPT: $CUTADAPT
echo SEQFU: $SEQFU

if [[ ! -z ${3+z} ]]; then
  R1=$1
  R2=$2
  OUTDIR=$3
  mkdir -p "$OUTDIR"

  B1=$(basename $R1)
  B2=$(basename $R2)
  echo "CUTADAPT $B1"

  cutadapt -a "${FOR}...${REVRC}" -A "${REV}...${FORRC}" $EXTRA \
     --minimum-length $MINL  \
     -o "$OUTDIR"/$B1 -p "$OUTDIR"/$B2 $R1 $R2
else
  echo USAGE: file_R1 file_R2 outdir
  exit
fi