#!/bin/bash -euo pipefail
mkdir -p rna_s1221_S42 && kallisto quant \
        --threads 4 \
        --index kallisto \
        --gtf Homo_sapiens.GRCh38.102.gtf \
         \
         \
         \
        --seed 1 \
        -o rna_s1221_S42 \
        rna_s1221_S42_1.fastp.fastq.gz rna_s1221_S42_2.fastp.fastq.gz 2> >(tee -a rna_s1221_S42/kallisto_quant.log >&2)

cp rna_s1221_S42/kallisto_quant.log rna_s1221_S42.log
cp rna_s1221_S42/abundance.h5 rna_s1221_S42.abundance.h5
cp rna_s1221_S42/abundance.tsv rna_s1221_S42.abundance.tsv
cp rna_s1221_S42/run_info.json rna_s1221_S42.run_info.json

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