#!/bin/bash -euo pipefail
tso500_detect_sample_type.py \
    --input 659_Bg-T1-TDNA-1_HLNN7DRX7_1_CombinedVariantOutput.tsv \
    --output 659_Bg-T1-TDNA-1_HLNN7DRX7_1.sample_type.txt

SAMPLE_TYPE=$(cat 659_Bg-T1-TDNA-1_HLNN7DRX7_1.sample_type.txt)

cat <<-END_VERSIONS > versions.yml
"NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_BIOMARKERS:HARMONIZE_BIOMARKERS_TSO500:TSO500_DETECT_SAMPLE_TYPE":
    python: $(python --version | sed 's/Python //')
    tso500_detect_sample_type: "1.0.0"
END_VERSIONS

# 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
#
echo SAMPLE_TYPE="${SAMPLE_TYPE[@]}" >> .command.env
echo /SAMPLE_TYPE/ >> .command.env