#!/bin/bash -euo pipefail
fusion_report run A673_FFPE_RNA_0001_B23LG7FLT4_3 . fusion_report_db --arriba A673_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.filtered_pass_only.tsv --starfusion A673_FFPE_RNA_0001_B23LG7FLT4_3.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv  --allow-multiple-gene-symbols --tool-cutoff 1 --export csv 

mv fusion_list.tsv A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport.tsv
mv fusion_list_filtered.tsv A673_FFPE_RNA_0001_B23LG7FLT4_3.fusionreport_filtered.tsv
mv index.html A673_FFPE_RNA_0001_B23LG7FLT4_3_fusionreport_index.html
[ ! -f fusions.csv ] || mv fusions.csv A673_FFPE_RNA_0001_B23LG7FLT4_3.fusions.csv
[ ! -f fusions.json ] || mv fusions.json A673_FFPE_RNA_0001_B23LG7FLT4_3.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