#!/bin/bash -euo pipefail
fusion_report run BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 . fusion_report_db --arriba BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.filtered_pass_only.tsv --starfusion BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv  --allow-multiple-gene-symbols --tool-cutoff 1 --export csv 

mv fusion_list.tsv BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.fusionreport.tsv
mv fusion_list_filtered.tsv BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.fusionreport_filtered.tsv
mv index.html BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_fusionreport_index.html
[ ! -f fusions.csv ] || mv fusions.csv BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.fusions.csv
[ ! -f fusions.json ] || mv fusions.json BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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