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#!/bin/bash
set -e
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a debian/tests/testdata.tar.xz "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
tar -xf testdata.tar.xz
OUTPUT_FILE_1="test1"
OUTPUT_FILE_2="test2"
gunzip -c reads.fastq.gz | NanoFilt -q 8 -l 500 --headcrop 50 > "$OUTPUT_FILE_1"
# Double check and make sure file is actually generated and is non-zero size
if [ -s "$OUTPUT_FILE_1" ];
then
echo "[1] PASS"
else
echo "[1] FAIL"
exit 1
fi
gunzip -c reads.fastq.gz | NanoFilt -q 7 --maxGC 0.75 --headcrop 75 | gzip > trimmed-reads.fastq.gz
echo "[2] PASS"
gunzip -c reads.fastq.gz | NanoFilt -q 6 -s sequencing_summary.txt > "$OUTPUT_FILE_2"
if [ -s "$OUTPUT_FILE_2" ];
then
echo "[3] PASS"
else
echo "[3] FAIL"
fi
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