#!/bin/bash -euo pipefail
inner_distance.py \
    -i 659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam 659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai \
    -r ref_annot.bed \
    -o 659_cIX-T1-TRNA-1_B23WHTKLT4_1 \
     \
    > stdout.txt
head -n 2 stdout.txt > 659_cIX-T1-TRNA-1_B23WHTKLT4_1.inner_distance_mean.txt

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