#!/bin/bash -euo pipefail
[ ! -f  BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastq.gz ] && ln -sf BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_R1.fastq.gz BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastq.gz
[ ! -f  BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastq.gz ] && ln -sf BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_R2.fastq.gz BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastq.gz
fastp \
    --in1 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastq.gz \
    --in2 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastq.gz \
    --out1 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz \
    --out2 BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz \
    --json BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.fastp.json \
    --html BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.fastp.html \
     \
     \
     \
    --thread 12 \
    --detect_adapter_for_pe \
    --reads_to_process 300000000  \
    2> BreastNB_FFPE_L03_RNA_01_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