// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]
options        = initOptions(params.options)

process APPYTER {
    tag "$meta.id"
    label 'process_medium'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

    // FIXME These rely on docker and won't work with conda
    // conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "$options.appyter_image"
    } else {
        container "$options.appyter_image}"
    }

    input:
    path input

    output:
    path "data/output.ipynb", emit: output_notebook
    path  "*.version.txt"   , emit: version

    script:
    // Add soft-links to original FastQs for consistent naming in pipeline
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"

    """
    appyter nbconstruct -i $input -o data/output.ipynb
    """
}