local_genepal

#!/usr/bin/env bash

NO_FORMAT="\033[0m"
C_RED="\033[38;5;9m"
F_BOLD="\033[1m"

profile="test_full"
stub=""
eggnogmapper_db_dir_param=""

for arg in "$@"; do
    case $arg in
        -stub)
            stub="-stub"
            ;;
        -test)
            profile="test"
            ;;
        -test_full)
            profile="test_full"
            ;;
    esac
done

if [[ -z $stub ]]; then
    echo -e "${C_RED}${F_BOLD}Executing without -stub${NO_FORMAT}"
fi

if [[ $profile == "test_full" ]]; then
    eggnogmapper_db_dir_param="--eggnogmapper_db_dir ../dbs/emapperdb/5.0.2"
    echo "Executing test_full"
else
    echo "Executing test"
fi

# Run nextflow with the selected flags
nextflow run \
    main.nf \
    -profile docker,${profile} \
    -resume \
    $stub \
    -c ../nxf-config/resources.config \
    $eggnogmapper_db_dir_param \
    --outdir results