#!/bin/bash -euo pipefail
mkdir -p BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2 \
        BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz 2> >(tee -a BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/kallisto_quant.log >&2)

cp BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/kallisto_quant.log BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.log
cp BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/abundance.h5 BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.abundance.h5
cp BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2/run_info.json BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.run_info.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:KALLISTO_QUANT":
    kallisto: $(echo $(kallisto version) | sed "s/kallisto, version //g" )
END_VERSIONS