#!/bin/bash -euo pipefail
mkdir -p tih_rna_sample_00104_23H5VFLT4_s20 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o tih_rna_sample_00104_23H5VFLT4_s20 \
        tih_rna_sample_00104_23H5VFLT4_s20_1.fastp.fastq.gz tih_rna_sample_00104_23H5VFLT4_s20_2.fastp.fastq.gz 2> >(tee -a tih_rna_sample_00104_23H5VFLT4_s20/kallisto_quant.log >&2)

cp tih_rna_sample_00104_23H5VFLT4_s20/kallisto_quant.log tih_rna_sample_00104_23H5VFLT4_s20.log
cp tih_rna_sample_00104_23H5VFLT4_s20/abundance.h5 tih_rna_sample_00104_23H5VFLT4_s20.abundance.h5
cp tih_rna_sample_00104_23H5VFLT4_s20/abundance.tsv tih_rna_sample_00104_23H5VFLT4_s20.abundance.tsv
cp tih_rna_sample_00104_23H5VFLT4_s20/run_info.json tih_rna_sample_00104_23H5VFLT4_s20.run_info.json

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