#!/usr/bin/env bash -C -e -u -o pipefail
bbnorm.sh \
    in=26Feb1256-C03.processed.fastq.gz,26Feb1256-A05.processed.fastq.gz,26Feb1256-C02.processed.fastq.gz,26Feb1256-B05.processed.fastq.gz,26Feb1256-E07.processed.fastq.gz,26Feb1256-D02.processed.fastq.gz,26Feb1256-C08.processed.fastq.gz,26Feb1256-A09.processed.fastq.gz,26Feb1256-E01.processed.fastq.gz,26Feb1256-D01.processed.fastq.gz,26Feb1256-E04.processed.fastq.gz,26Feb1256-H03.processed.fastq.gz,26Feb1256-E08.processed.fastq.gz,26Feb1256-B08.processed.fastq.gz,26Feb1256-A07.processed.fastq.gz,26Feb1256-C05.processed.fastq.gz,26Feb1256-H02.processed.fastq.gz,26Feb1256-E02.processed.fastq.gz,26Feb1256-G02.processed.fastq.gz,26Feb1256-E05.processed.fastq.gz,26Feb1256-H06.processed.fastq.gz,26Feb1256-G04.processed.fastq.gz,26Feb1256-F05.processed.fastq.gz,26Feb1256-B09.processed.fastq.gz,26Feb1256-E03.processed.fastq.gz,26Mar681-H01.processed.fastq.gz,26Feb1256-B03.processed.fastq.gz,26Feb1256-A10.processed.fastq.gz,26Feb1256-D03.processed.fastq.gz,26Feb1256-G08.processed.fastq.gz,26Feb1256-F08.processed.fastq.gz,26Feb1256-D06.processed.fastq.gz,26Feb1256-A04.processed.fastq.gz,26Feb1256-C06.processed.fastq.gz,26Feb1256-H04.processed.fastq.gz,26Feb1256-D09.processed.fastq.gz,26Feb1256-E06.processed.fastq.gz,26Feb1256-H01.processed.fastq.gz,26Feb1256-A01.processed.fastq.gz,26Feb1256-F07.processed.fastq.gz,26Feb1256-A02.processed.fastq.gz,26Feb1256-B01.processed.fastq.gz,26Feb1256-A06.processed.fastq.gz,26Feb1256-G07.processed.fastq.gz,26Feb1256-H05.processed.fastq.gz,26Feb1256-C07.processed.fastq.gz,26Feb1256-B04.processed.fastq.gz,26Mar681-D01.processed.fastq.gz,26Feb1256-F10.processed.fastq.gz,26Feb1256-F03.processed.fastq.gz,26Feb1256-H07.processed.fastq.gz,26Feb1256-G06.processed.fastq.gz,26Feb1256-D05.processed.fastq.gz,26Feb1256-H08.processed.fastq.gz,26Feb1256-F04.processed.fastq.gz,26Feb1256-B02.processed.fastq.gz,26Mar681-C03.processed.fastq.gz,26Mar681-E04.processed.fastq.gz,26Mar681-E03.processed.fastq.gz,26Mar681-C02.processed.fastq.gz,26Mar681-F02.processed.fastq.gz,26Mar681-B02.processed.fastq.gz,26Mar681-D03.processed.fastq.gz,26Mar681-A02.processed.fastq.gz,26Mar681-H03.processed.fastq.gz,26Mar681-A04.processed.fastq.gz,26Feb1256-D04.processed.fastq.gz,26Mar681-G04.processed.fastq.gz,26Feb1256-B07.processed.fastq.gz,26Feb1256-A08.processed.fastq.gz,26Mar681-D04.processed.fastq.gz,26Feb1256-G09.processed.fastq.gz,26Mar681-F04.processed.fastq.gz,26Mar681-B04.processed.fastq.gz,26Feb1256-F02.processed.fastq.gz,26Feb1256-E09.processed.fastq.gz,26Feb1256-F06.processed.fastq.gz,26Feb1256-E11.processed.fastq.gz,26Feb1256-F09.processed.fastq.gz,26Feb1256-G03.processed.fastq.gz,26Feb1256-D07.processed.fastq.gz,26Feb1256-C10.processed.fastq.gz,26Feb1256-C01.processed.fastq.gz,26Feb1256-C09.processed.fastq.gz,26Feb1256-D08.processed.fastq.gz,26Mar681-G01.processed.fastq.gz,26Feb1256-A03.processed.fastq.gz,26Mar681-B03.processed.fastq.gz,26Feb1256-C11.processed.fastq.gz,26Mar681-G03.processed.fastq.gz,26Feb1256-D10.processed.fastq.gz,26Feb1256-H09.processed.fastq.gz,26Feb1256-C04.processed.fastq.gz,26Feb1256-A11.processed.fastq.gz,26Feb1256-B06.processed.fastq.gz,26Feb1256-F01.processed.fastq.gz,26Feb1256-G01.processed.fastq.gz,26Feb1256-G05.processed.fastq.gz,26Mar681-F03.processed.fastq.gz,26Feb1256-G10.processed.fastq.gz,26Feb1256-D11.processed.fastq.gz,26Feb1256-B10.processed.fastq.gz,26Mar681-G02.processed.fastq.gz,26Mar681-E05.processed.fastq.gz,26Mar681-A05.processed.fastq.gz,26Mar681-A01.processed.fastq.gz,26Mar681-B05.processed.fastq.gz,26Mar681-A03.processed.fastq.gz,26Mar681-C01.processed.fastq.gz,26Feb1256-H10.processed.fastq.gz,26Mar681-E02.processed.fastq.gz,26Mar681-G05.processed.fastq.gz,26Feb1256-E10.processed.fastq.gz,26Mar681-F05.processed.fastq.gz,26Mar681-H05.processed.fastq.gz,26Mar681-H04.processed.fastq.gz,26Mar681-A06.processed.fastq.gz,26Mar681-E01.processed.fastq.gz,26Feb1256-B11.processed.fastq.gz,26Mar681-D05.processed.fastq.gz,26Mar681-H02.processed.fastq.gz,26Mar681-D02.processed.fastq.gz,26Mar681-F01.processed.fastq.gz,26Mar681-C04.processed.fastq.gz,26Mar681-C05.processed.fastq.gz,26Mar681-B01.processed.fastq.gz \
    out=all_samples.fastq.gz \
    target=50 min=5 \
    threads=6 \
    -Xmx819g \
    &> all_samples.bbnorm.log

# capture process environment
set +u
set +e
cd "$NXF_TASK_WORKDIR"

nxf_eval_cmd() {
    {
        IFS=$'\n' read -r -d '' "${1}";
        IFS=$'\n' read -r -d '' "${2}";
        (IFS=$'\n' read -r -d '' _ERRNO_; return ${_ERRNO_});
    } < <((printf '\0%s\0%d\0' "$(((({ shift 2; "${@}"; echo "${?}" 1>&3-; } | tr -d '\0' 1>&4-) 4>&2- 2>&1- | tr -d '\0' 1>&4-) 3>&1- | exit "$(cat)") 4>&1-)" "${?}" 1>&2) 2>&1)
}

echo '' > .command.env
#
nxf_eval_cmd STDOUT STDERR bash -c "bbversion.sh | grep -v \"Duplicate cpuset\""
status=$?
if [ $status -eq 0 ]; then
  echo nxf_out_eval_22="$STDOUT" >> .command.env
  echo /nxf_out_eval_22/=exit:0 >> .command.env
else
  echo nxf_out_eval_22="$STDERR" >> .command.env
  echo /nxf_out_eval_22/=exit:$status >> .command.env
fi