#!/bin/bash -euo pipefail
infer_experiment.py \
    -i HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
     \
    > HD789_0002_RNA_0008_23H5VFLT4_s19.infer_experiment.txt

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