#!/bin/bash -euo pipefail
printf "%s %s\n" SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_trimmed_1.gz SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_trimmed_2.gz | while read old_name new_name; do
    [ -f "${new_name}" ] || ln -s $old_name $new_name
done

fastqc \
    --quiet \
    --threads 2 \
    SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_trimmed_1.gz SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1_trimmed_2.gz

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