#!/bin/bash -euo pipefail
printf "%s %s\n" SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_R1.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_1.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_R2.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_2.gz | while read old_name new_name; do
    [ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc \
    --quiet \
    --threads 2 \
    SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_1.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3_2.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:FASTQC":
    fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS