#!/bin/bash -euo pipefail
mkdir -p NTC_0001_0001_23H5VFLT4_s15 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o NTC_0001_0001_23H5VFLT4_s15 \
        NTC_0001_0001_23H5VFLT4_s15_1.fastp.fastq.gz NTC_0001_0001_23H5VFLT4_s15_2.fastp.fastq.gz 2> >(tee -a NTC_0001_0001_23H5VFLT4_s15/kallisto_quant.log >&2)

cp NTC_0001_0001_23H5VFLT4_s15/kallisto_quant.log NTC_0001_0001_23H5VFLT4_s15.log
cp NTC_0001_0001_23H5VFLT4_s15/abundance.h5 NTC_0001_0001_23H5VFLT4_s15.abundance.h5
cp NTC_0001_0001_23H5VFLT4_s15/abundance.tsv NTC_0001_0001_23H5VFLT4_s15.abundance.tsv
cp NTC_0001_0001_23H5VFLT4_s15/run_info.json NTC_0001_0001_23H5VFLT4_s15.run_info.json

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