#!/bin/bash -euo pipefail
picard \
    -Xmx4096M -XX:+UseParallelGC -XX:ParallelGCThreads=1 \
    CollectRnaSeqMetrics \
    --TMP_DIR ./tmp \
    --STRAND_SPECIFICITY NONE \
    --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list \
    --REF_FLAT ref_annot.gtf.refflat \
    --INPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam \
    --OUTPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1_rna_metrics.txt \

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:QC_WORKFLOW:PICARD_COLLECTRNASEQMETRICS":
    picard: $(picard CollectRnaMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS