#!/bin/bash -euo pipefail
run_level_intermediate.py \
    --flowcell-qc "flowcell_qc.csv" \
    --demux-stats "Demultiplex_Stats_aggregate.csv" \
    --controls-tsv "multiqc_general_stats_controls.tsv" \
    --sample-type-map "sample_type_map.csv" \
    --fusion-vcfs FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.fusion_data.vcf.gz --fusion-vcfs FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.fusion_data.vcf.gz \
    --truth-data positive_control_truth_data.fusion.csv \
    --pipeline-version "rnafusion_3.0.2-gunknown" \
    -o run_level_intermediate.tsv

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:RUN_LEVEL_INTERMEDIATE":
    python: $(python3 --version | sed 's/Python //g')
    run_level_intermediate: 1.1.0
END_VERSIONS