#!/bin/bash -euo pipefail
printf "%s %s\n" GM24385_0001_RNA_0001_23H5VFLT4_s32_R1.fastq.gz GM24385_0001_RNA_0001_23H5VFLT4_s32_1.gz GM24385_0001_RNA_0001_23H5VFLT4_s32_R2.fastq.gz GM24385_0001_RNA_0001_23H5VFLT4_s32_2.gz | while read old_name new_name; do
    [ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc \
    --quiet \
    --threads 2 \
    GM24385_0001_RNA_0001_23H5VFLT4_s32_1.gz GM24385_0001_RNA_0001_23H5VFLT4_s32_2.gz

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