#!/bin/bash -euo pipefail
junction_annotation.py \
    -i BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1 \
     \
    2> >(grep -v 'E::idx_find_and_load' | tee BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.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