#!/bin/bash -euo pipefail
printf "%s %s\n" SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2_trimmed_1.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2_trimmed_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_2_trimmed_1.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2_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