#!/bin/bash -euo pipefail
fusion_report run BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 . fusion_report_db --arriba BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv --starfusion BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv  --allow-multiple-gene-symbols --tool-cutoff 1 --export csv 

mv fusion_list.tsv BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.fusionreport.tsv
mv fusion_list_filtered.tsv BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.fusionreport_filtered.tsv
mv index.html BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_fusionreport_index.html
[ ! -f fusions.csv ] || mv fusions.csv BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.fusions.csv
[ ! -f fusions.json ] || mv fusions.json BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.fusions.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FUSIONREPORT_WORKFLOW:FUSIONREPORT":
    fusion_report: $(fusion_report --version | sed 's/fusion-report //')
    fusion_report DB retrieval: $(cat fusion_report_db/DB-timestamp.txt)
END_VERSIONS