main.nf

params.repo_url = null

process CloneRepository {
    output:
    path 'repo_path'

    publishDir '.', mode: 'copy'

    script:
    """
    if [ -z "${params.repo_url}" ]; then
        echo "Error: Please provide a repository URL using '--repo_url <repository-url>'"
        exit 1
    fi
    echo "Cloning repository from ${params.repo_url}"
    mkdir -p repo
    git clone ${params.repo_url} repo
    ls -la repo
    echo "repo_path=${PWD}/repo" > repo_path
    """
}

// process CheckDependencies {
//     input:
//     path repo_path

//     script:
//     """
//     cd ${repo_path}
//     if [ -f requirements.txt ]; then
//         echo "Found requirements.txt"
//     elif [ -f environment.yml ]; then
//         echo "Found environment.yml"
//     elif [ -f package.json ]; then
//         echo "Found package.json"
//     else
//         echo "No dependency files found" >&2
//         exit 1
//     fi
//     """
// }

workflow {
    // Debugging output
    println "Workflow starting with repo_url: ${params.repo_url}"

    if (!params.repo_url) {
        error "Please provide a repository URL using '--repo_url <repository-url>'"
    }

    // Execute processes
    def clonedRepo = CloneRepository()
    // CheckDependencies(clonedRepo.repo_path)
}