#!/bin/bash

set -eo pipefail

mkdir -p $par_output

Rscript "$meta_resources_dir/summarizedexperiment.r" NULL $par_counts_gene $par_tpm_gene $par_tx2gene_tsv 

Rscript "$meta_resources_dir/summarizedexperiment.r" NULL $par_counts_gene_length_scaled $par_tpm_gene $par_tx2gene_tsv 

Rscript "$meta_resources_dir/summarizedexperiment.r" NULL $par_counts_gene_scaled $par_tpm_gene $par_tx2gene_tsv 

Rscript "$meta_resources_dir/summarizedexperiment.r" NULL $par_counts_transcript $par_tpm_transcript $par_tx2gene_tsv 

mv ${par_counts_gene%.*}.rds $par_output/
mv ${par_counts_gene_length_scaled%.*}.rds $par_output/
mv ${par_counts_gene_scaled%.*}.rds $par_output/
mv ${par_counts_transcript%.*}.rds $par_output/
