#!/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_01_RNA_13_B23WHTKLT4_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