#!/bin/bash -euo pipefail
infer_experiment.py \
    -i BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
     \
    > BT-20_FFPE_RNA_0001_B23LG7FLT4_1.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