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

// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
//               https://github.com/nf-core/modules/tree/master/software
//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
//               https://nf-co.re/join

// TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
// 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.
// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
//               unless there is a run-time, storage advantage in implementing in this way
//               e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.

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

process SEQKIT_SPLIT2 {
    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) }

    conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)

    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
    } else {
        container "quay.io/biocontainers/seqkit:0.15.0--0"
    }

    input:
    tuple val(meta), path(read1), path(read2)

    // 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.

    output:
    tuple val(meta), path("*.fq.gz"), emit: reads
    path("*.version.txt")          , emit: version


    script:
    def software = getSoftwareName(task.process)

    //TODO not sure if this is useful here, as the splits need to be named individually, and this would make the prefix the same and the outputname I am afraid.
    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

    if(meta.single_end){ //TODO: I guess since optionally inputs are not possible right now, we need two modules, one for single_end and one for paired_end
    """
    seqkit \
        split2 \
        $options.args \
        --threads $task.cpus \
        -1 $read1 \
        -O $prefix


    echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
    """
    } else {
    """
    seqkit \
        split2 \
        $options.args \
        --threads $task.cpus \
        -1 $read1 \
        -2 $read2 \
        -O $prefix

    echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
    """
    }
}