#!/bin/bash -euo pipefail
samtools \
    view \
    --threads 3 \
    --reference ref_genome.fa \
     \
    --output-fmt cram \
    -o 659_ciJ-T1-TRNA-1_B23WHTKLT4_1.star_alignment.Aligned.sortedByCoord.out.cram \
    659_ciJ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam \


cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS