#!/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 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam \
--OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_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