#!/bin/bash
set -e

pkg="trim-galore"

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

cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP

echo 'Test 1'
trim_galore --paired --three_prime_clip_R1 15 --three_prime_clip_R2 15 clock_10K_R1.fastq.gz clock_10K_R2.fastq.gz

echo 'Test 2'
trim_galore --illumina illumina*.gz

echo 'Test 3'
trim_galore --trim-n --fastqc --fastqc_args "--nogroup" 4_seqs_with_Ns.fastq.gz

echo 'Test 4'
trim_galore --small_rna --trim-n smallRNA_100K.fastq.gz

echo 'Test 5'
trim_galore -e 0.15 --max_n 10 smallRNA_100K.fastq.gz
