#!/bin/bash

set -e

### Note: don't actually run this -- this script is just
# a record of how / in what order to run the other scripts.


# needed for predicting with ProCapNet
GPU="1"

cell_types=( "K562" "A673" "CACO2" "CALU3" "HUVEC" "MCF10A" )

chroms=( "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22" "chrX" "chrY")


for cell_type in "${cell_types[@]}"; do
  for chrom in "${chroms[@]}"; do
    ./v1_predict_hg38.sh "$cell_type" "$chrom" "$GPU" || exit 1
    ./v1_process_preds.sh "$cell_type" "$chrom"  || exit 1

    #./v1_delete_raw_files.sh "$cell_type" "$chrom"
  done
  
  # run after you've got predictions for all the chromosomes in a cell type
  python v1_merge_chrom_bigwigs_to_make_genomewide_bigwigs.py "$cell_type" || exit 1
done

exit 0