#!/bin/bash -euo pipefail
junction_annotation.py \
    -i rna_s1221_S42.Aligned.sortedByCoord.out.bam rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o rna_s1221_S42 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee rna_s1221_S42.junction_annotation.log >&2)

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION":
    rseqc: $(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
END_VERSIONS