#!/bin/bash -euo pipefail
fusion_report run tih_rna_sample_00088_23H5VFLT4_s02 . fusion_report_db --arriba tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.filtered_pass_only.tsv --starfusion tih_rna_sample_00088_23H5VFLT4_s02.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv  --allow-multiple-gene-symbols --tool-cutoff 1 --export csv 

mv fusion_list.tsv tih_rna_sample_00088_23H5VFLT4_s02.fusionreport.tsv
mv fusion_list_filtered.tsv tih_rna_sample_00088_23H5VFLT4_s02.fusionreport_filtered.tsv
mv index.html tih_rna_sample_00088_23H5VFLT4_s02_fusionreport_index.html
[ ! -f fusions.csv ] || mv fusions.csv tih_rna_sample_00088_23H5VFLT4_s02.fusions.csv
[ ! -f fusions.json ] || mv fusions.json tih_rna_sample_00088_23H5VFLT4_s02.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