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#!/bin/sh
set -e
set -u
root=$(mktemp --tmpdir -d "pigx.XXXX")
testfolder=${root}/tests/test_genome_coverage
mkdir -p ${testfolder}
echo "TEST FOLDER: ${testfolder}"
# copy necessary input files to the test folder
# we copy them to avoid re-creating these files when testing the pipeline
cp -r ${srcdir}/tests/sample_data/preprocessed/mapped_reads/ ${testfolder}
# make these copies writable
chmod +w -R ${testfolder}
# prepare temporary sample sheet and settings files
settings=${srcdir}/tests/settings_no_de.yaml
tmp_settings="${testfolder}/settings.yaml"
sed -e "s,reads-dir: ,reads-dir: ${srcdir}/tests/,g" \
-e "s,genome-fasta: ,genome-fasta: ${srcdir}/tests/,g" \
-e "s,cdna-fasta: ,cdna-fasta: ${srcdir}/tests/,g" \
-e "s,gtf-file: ,gtf-file: ${srcdir}/tests/,g" \
-e "s,output-dir:.*,output-dir: ${testfolder},g" \
${settings} > ${tmp_settings}
#create links to already preprocessed sample data
samplesheet=${srcdir}/tests/sample_sheet.csv
tmp_samplesheet="${testfolder}/sample_sheet.csv"
head -n 2 ${samplesheet} > ${tmp_samplesheet}
${builddir}/pigx-rnaseq -s ${tmp_settings} --target genome_coverage ${tmp_samplesheet}
rm ${tmp_settings} ${tmp_samplesheet}
rm -rf ${testfolder}/mapped_reads/
if ! test -f ${testfolder}/bigwig_files/HBR_Rep1.forward.bigwig
then
echo "ERROR: failed to create bigwig file from input BAM file"
exit 1
fi
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