#!/bin/sh -e

pkg=trimmomatic

if [ "$ADTTMP" = "" ] ; then
  ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
fi

cd $ADTTMP

cp -a /usr/share/doc/${pkg}/test_data/* .
gunzip -r *

TrimmomaticSE -phred33 test_single.fq out.fq \
	ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 \
	LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 \
	MINLEN:36

TrimmomaticPE -phred33 test_forward.fq test_reverse.fq \
	out_forward_paired.fq out_forward_unpaired.fq \
	out_reverse_paired.fq out_reverse_unpaired.fq \
	ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 \
	TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

TrimmomaticPE -phred33 test_forward.fq test_reverse.fq \
	out_forward_paired.fq out_forward_unpaired.fq \
	out_reverse_paired.fq out_reverse_unpaired.fq \
	ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 \
	TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
