#!/bin/bash -euo pipefail
arriba \
    -x 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam \
    -a ref_genome.fa \
    -g ref_annot.gtf \
    -o 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.tsv \
    -O 1173_H2E_T1_RNA_SLD_01_A23T55JLT4_1.arriba.fusions.discarded.tsv \
    -b blacklist_hg38_GRCh38_v2.4.0.tsv.gz \
    -k known_fusions_hg38_GRCh38_v2.4.0.tsv.gz \
     \
     \
    -p protein_domains_hg38_GRCh38_v2.4.0.gff3 \


cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA":
    arriba: $(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version: //')
END_VERSIONS