#!/bin/bash

DELIVERY_FOLDER="$(date '+%Y%m%d')_entrega01"

mkdir -p "${DELIVERY_FOLDER}/characterization/amrfinderplus"
mkdir -p "${DELIVERY_FOLDER}/characterization/emmtyper"

# ARIBA characterization service
cd $DELIVERY_FOLDER/characterization
ln -s ../../../ANALYSIS/*CHARACTERIZATION/99-stats/ariba_*.tsv .
ln -s ../../../ANALYSIS/*CHARACTERIZATION/99-stats/ariba_*.csv .

cd amrfinderplus
ln -s ../../../../ANALYSIS/*CHARACTERIZATION/*amrfinderplus/*tsv .
find .. -xtype l -delete

cd ..
cd emmtyper
ln -s ../../../../ANALYSIS/*CHARACTERIZATION/*emmtyper/01-typing/results_emmtyper.out .

cd ../../../

eval "$(micromamba shell hook --shell=bash)"
micromamba activate outbreakinfo

python3 generate_summary_outbreak.py

mv summary_outbreak_filled.xlsx $DELIVERY_FOLDER

micromamba deactivate