#!/bin/bash -euo pipefail
vcf_collect.py \
--fusioninspector A673_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect \
--fusionreport A673_FFPE_RNA_0001_B23LG7FLT4_1_fusionreport_index.html \
--fusioninspector_gtf A673_FFPE_RNA_0001_B23LG7FLT4_1.tsv \
--fusionreport_csv A673_FFPE_RNA_0001_B23LG7FLT4_1.fusions.csv \
--hgnc hgnc_complete_set.txt \
--sample A673_FFPE_RNA_0001_B23LG7FLT4_1 \
--out A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_data.vcf \
--arriba_fusions A673_FFPE_RNA_0001_B23LG7FLT4_1.arriba.fusions.filtered_pass_only.tsv \
--use_chr_prefix

sort_fusion_vcf_mateid.py \
--input A673_FFPE_RNA_0001_B23LG7FLT4_1.fusion_data.vcf

bgzip A673_FFPE_RNA_0001_B23LG7FLT4_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