#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE   } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ]  )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART   } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-part 3']    )

workflow test_seqkit_split2_single_end_length {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_LENGTH ( input )
}

workflow test_seqkit_split2_single_end_size {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_SIZE ( input )
}

workflow test_seqkit_split2_single_end_part {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_PART ( input )
}

workflow test_seqkit_split2_paired_end_length {
    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_LENGTH ( input )
}

workflow test_seqkit_split2_paired_end_size {
    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_SIZE ( input )
}

workflow test_seqkit_split2_paired_end_part {
    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
              file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
            ]

    SEQKIT_SPLIT2_PART ( input )
}