#!/bin/bash -euo pipefail
printf "%s %s\n" BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_R1.fastq.gz BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_1.gz BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_R2.fastq.gz BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_2.gz | while read old_name new_name; do
[ -f "${new_name}" ] || ln -s $old_name $new_name
done
fastqc \
--quiet \
--threads 2 \
BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_1.gz BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2_2.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FASTQC":
fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS