#!/bin/bash -Ceuo pipefail
cat << 'EOF' > manifest.json
{"pairs":[{"pair_id":"659_csY-T1-TDNA-1_A23FG3YLT4_1_vs_659_csY-N1-BDNA-1_A23FG3YLT4_1","tumor_sample":"659_csY-T1-TDNA-1_A23FG3YLT4_1","normal_sample":"659_csY-N1-BDNA-1_A23FG3YLT4_1"},{"pair_id":"659_eHw-T1-TDNA-1_B23MCVGLT4_1_vs_659_eHw-N1-BDNA-1_B23KFG5LT4_1","tumor_sample":"659_eHw-T1-TDNA-1_B23MCVGLT4_1","normal_sample":"659_eHw-N1-BDNA-1_B23KFG5LT4_1"},{"pair_id":"659_gK-T1-TDNA-1_A23MCTVLT4_1_vs_659_gK-N1-BDNA-1_B23KFG5LT4_1","tumor_sample":"659_gK-T1-TDNA-1_A23MCTVLT4_1","normal_sample":"659_gK-N1-BDNA-1_B23KFG5LT4_1"}],"qc_files":[]}
EOF

    aggregate_qc_metrics.py \
        --manifest manifest.json \
        --files-dir . \
        --output variant_qc.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:AGGREGATE_VARIANT_QC":
    python: $(python --version | sed 's/Python //g')
    aggregate_qc_metrics: 2.0.0
END_VERSIONS