#!/bin/bash -euo pipefail
mkdir -p FFPE_HD789_01_RNA_13_B23MVV7LT4_1 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o FFPE_HD789_01_RNA_13_B23MVV7LT4_1 \
        FFPE_HD789_01_RNA_13_B23MVV7LT4_1_1.fastp.fastq.gz FFPE_HD789_01_RNA_13_B23MVV7LT4_1_2.fastp.fastq.gz 2> >(tee -a FFPE_HD789_01_RNA_13_B23MVV7LT4_1/kallisto_quant.log >&2)

cp FFPE_HD789_01_RNA_13_B23MVV7LT4_1/kallisto_quant.log FFPE_HD789_01_RNA_13_B23MVV7LT4_1.log
cp FFPE_HD789_01_RNA_13_B23MVV7LT4_1/abundance.h5 FFPE_HD789_01_RNA_13_B23MVV7LT4_1.abundance.h5
cp FFPE_HD789_01_RNA_13_B23MVV7LT4_1/abundance.tsv FFPE_HD789_01_RNA_13_B23MVV7LT4_1.abundance.tsv
cp FFPE_HD789_01_RNA_13_B23MVV7LT4_1/run_info.json FFPE_HD789_01_RNA_13_B23MVV7LT4_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