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

// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
//               All other parameters MUST be provided as a string i.e. "options.args"
//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
//               Any parameters that need to be evaluated in the context of a particular sample
//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.

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

process MAXQUANT_LFQ {
    tag "$meta.id"
    label 'process_long'
    publishDir "${params.outdir}",
        mode: params.publish_dir_mode,
        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

    conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
    } else {
        container "quay.io/biocontainers/quay.io/biocontainers/maxquant:2.0.1.0--py39hdfd78af_2"
    }

    input:
    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
    //               MUST be provided as an input via a Groovy Map called "meta".
    //               This information may not be required in some instances e.g. indexing reference genome files:
    //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
    tuple val(meta), path(raw), path(paramfile)

    output:
    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
    tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt
    // TODO nf-core: List additional required output channels/values here
    path "*.version.txt"          , emit: version

    script:
    def software = getSoftwareName(task.process)
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
    //               If the software is unable to output a version number on the command-line then it can be manually specified
    //               e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
    // TODO nf-core: Please replace the example samtools command below with your module's command
    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
    """
    maxquant --version > maxquant.version.txt
    # Write number of threads into parameter file
    sed "s_\<numThreads\>.*_\<numThreads\>12\<\/numThreads\>_" ${paramfile}
    # Correct folder names
    sed -i "s|PLACEHOLDER|\$PWD/|g" "${paramfile}"
    mkdir temp
  
    maxquant ${paramfile}
    """
}