#!/bin/bash -euo pipefail
mkdir -p A549_FFPE_01_RNA_0001_B23LG7FLT4_1 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o A549_FFPE_01_RNA_0001_B23LG7FLT4_1 \
        A549_FFPE_01_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz A549_FFPE_01_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz 2> >(tee -a A549_FFPE_01_RNA_0001_B23LG7FLT4_1/kallisto_quant.log >&2)

cp A549_FFPE_01_RNA_0001_B23LG7FLT4_1/kallisto_quant.log A549_FFPE_01_RNA_0001_B23LG7FLT4_1.log
cp A549_FFPE_01_RNA_0001_B23LG7FLT4_1/abundance.h5 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.abundance.h5
cp A549_FFPE_01_RNA_0001_B23LG7FLT4_1/abundance.tsv A549_FFPE_01_RNA_0001_B23LG7FLT4_1.abundance.tsv
cp A549_FFPE_01_RNA_0001_B23LG7FLT4_1/run_info.json A549_FFPE_01_RNA_0001_B23LG7FLT4_1.run_info.json

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