#!/bin/bash -euo pipefail
mkdir -p GM24385_0001_RNA_0001_23H5VFLT4_s40 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o GM24385_0001_RNA_0001_23H5VFLT4_s40 \
        GM24385_0001_RNA_0001_23H5VFLT4_s40_1.fastp.fastq.gz GM24385_0001_RNA_0001_23H5VFLT4_s40_2.fastp.fastq.gz 2> >(tee -a GM24385_0001_RNA_0001_23H5VFLT4_s40/kallisto_quant.log >&2)

cp GM24385_0001_RNA_0001_23H5VFLT4_s40/kallisto_quant.log GM24385_0001_RNA_0001_23H5VFLT4_s40.log
cp GM24385_0001_RNA_0001_23H5VFLT4_s40/abundance.h5 GM24385_0001_RNA_0001_23H5VFLT4_s40.abundance.h5
cp GM24385_0001_RNA_0001_23H5VFLT4_s40/abundance.tsv GM24385_0001_RNA_0001_23H5VFLT4_s40.abundance.tsv
cp GM24385_0001_RNA_0001_23H5VFLT4_s40/run_info.json GM24385_0001_RNA_0001_23H5VFLT4_s40.run_info.json

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