#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
include '../main.nf' params(params)

// Define input channels
paired_end_input = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )

// TODO: params.single_end is set to false in nextflow config
// But most of this module is not functional currently anyway....
single_end_input = Channel.from([
        ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
        ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
        ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
        ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
    ]).map { row -> [ row[0], [ file(row[1]) ] ] }

// Run the workflow
workflow {
    cutadapt(paired_end_input)
    cutadapt(single_end_input)
}