#!/bin/bash -euo pipefail
mkdir -p 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2 \
        1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz 2> >(tee -a 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/kallisto_quant.log >&2)

cp 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/kallisto_quant.log 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.log
cp 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/abundance.h5 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.abundance.h5
cp 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/abundance.tsv 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.abundance.tsv
cp 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2/run_info.json 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.run_info.json

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