main

#!/bin/bash

set -euo pipefail

function on_failure {
    echo "The script" "${0##*/}" "has failed"
}

trap on_failure ERR

source ./scripts/getopts

# housekeeping
declare -a SCRIPTS=(
"preamble.R"
"create-object-sct.R"
"integrate.R"
)

# do check for multimodal routine
if [[ "${atac:-}" == "TRUE" ]]
then
    echo "Running ATAC-multiome WNN Preprocessing"
    SCRIPTS=("preamble.R" "atac-multi-wnn.R")
    echo "${SCRIPTS[@]}"
elif [[ "${cite:-}" == "TRUE" ]]
then
    echo "Running CITE-multiome WNN Preprocessing"
    SCRIPTS=("preamble.R" "cite-wnn.R")
    echo "${SCRIPTS[@]}"
elif [[ "${harmonize:-}" == "TRUE" ]]
then
    echo "Integrating using Harmony"
    SCRIPTS=("preamble.R" "create-object-sct.R" "harmonize.R")
    echo "${SCRIPTS[@]}"
elif [[ "${mixscape:-}" == "TRUE" ]]
then
    echo "Running Mixscape Perturbation Preprocessing"
    SCRIPTS=("preamble.R" "create-multi-norm.R" "mixscape.R")
    echo "${SCRIPTS[@]}"
else
    echo "Creating traditional Seurat object"
fi

# execute pipeline scripts
for i in "${SCRIPTS[@]}"
do
    echo "coreSC master version commit $(cat .git/refs/heads/master | cut -c -7)" >> "$OUT_DIR"/log.txt
    Rscript ./scripts/"$i" "$OUT_DIR" 2>&1 | tee -a "$OUT_DIR"/log.txt
done

cp ./config/params.csv ./config/samples.csv "$OUT_DIR"
rm -rf "$OUT_DIR"/tmp