#!/bin/bash -euo pipefail
vcf_collect.py \
--fusioninspector 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect \
--fusionreport 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1_fusionreport_index.html \
--fusioninspector_gtf 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.tsv \
--fusionreport_csv 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.fusions.csv \
--hgnc hgnc_complete_set.txt \
--sample 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1 \
--out 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.fusion_data.vcf \
--arriba_fusions 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.filtered_pass_only.tsv \
--use_chr_prefix

sort_fusion_vcf_mateid.py \
--input 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.fusion_data.vcf

bgzip 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.fusion_data.vcf

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT":
    python: $(python --version | sed 's/Python //g')
    HGNC DB retrieval: $(cat HGNC-DB-timestamp.txt)
END_VERSIONS