#!/bin/bash -euo pipefail
[ ! -f  SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastq.gz ] && ln -sf SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_R1.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastq.gz
[ ! -f  SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastq.gz ] && ln -sf SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_R2.fastq.gz SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastq.gz
fastp \
    --in1 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastq.gz \
    --in2 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastq.gz \
    --out1 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz \
    --out2 SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz \
    --json SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.fastp.json \
    --html SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.fastp.html \
     \
     \
     \
    --thread 12 \
    --detect_adapter_for_pe \
    --reads_to_process 300000000  \
    2> SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.fastp.log

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:TRIM_WORKFLOW:FASTP":
    fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS