#!/usr/bin/env nextflow

nextflow.preview.dsl = 2

params.out_dir = "test_output"
params.fastqc_args = ''
params.publish_dir_mode = "copy"
params.bedtools_genomecov_args = '' //'-bg'

include BEDTOOLS_GENOMECOV from '../main.nf' params(params)

// Define input channels
ch_input = Channel.fromPath('./input_data/JK2067_downsampled_s0.1.bam')
chrom_sizes = Channel.fromPath('./input_data/genome.sizes')

// Run the workflow
workflow {
    BEDTOOLS_GENOMECOV(ch_input, chrom_sizes, params.bedtools_genomecov_args)
}