#!/bin/bash
set -ex

pkg=packagename
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
	AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
fi
cd "$AUTOPKGTEST_TMP"

cp -a /usr/share/doc/shovill-examples/* "$AUTOPKGTEST_TMP"
cd "$AUTOPKGTEST_TMP"

shovill --adapters trimmomatic.fa --outdir out --R1 R1.fq.gz --R2 R2.fq.gz
ls out/
head -n 4 out/contigs.fa
