test.sh.in

#!@GNUBASH@

set -e
set -u

export SOURCE_DATE_EPOCH=1
export PIGX_UGLY=1
export PIGX_UNINSTALLED=1

# We do not use "readlink -f" here, because macos does not support it.
export srcdir=$(@PYTHON@ -c 'import os,sys; print(os.path.realpath(sys.argv[1]))' ${srcdir:-.})

chmod -R +w ${srcdir}/tests

./pigx-bsseq -s ${srcdir}/tests/settings.yaml ${srcdir}/tests/sample_sheet.csv \
    --printshellcmds --target={final-report-bwameth,final-report}

for base in PEsample_wgbs_1_val_1_bt2 SEsample_se_bt2 SEsample_v2_se_bt2; do
    if ! test -f "${srcdir}/tests/out/Reports/sample_reports/${base}.sorted.deduped_cpg_methylKit_hg19_final.html"
    then
        echo "ERROR: could not find bismark report for ${base}"
        exit 1
    fi
done

for base in PEsample_wgbs SEsample SEsample_v2; do
    if ! test -f "${srcdir}/tests/out/Reports/sample_reports/${base}.deduped_CpG_methylDackel_hg19_final.html"
    then
        echo "ERROR: could not find bwameth report for ${base}"
        exit 1
    fi
done