main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { SELECT_SAMPLES } from './modules/local/select_samples.nf'

params.samples_tsv = "input/input_data.tsv"

Channel 
    .fromPath( params.samples_tsv )
    .splitCsv( header: true, sep: '\t' )
    .set { input_data_ch }

Channel
    .empty()
    .mix( input_data_ch
              .filter { it.dataset_name == "consensus_element_counts" }
              .map { it -> file( it.dataset_path ) } )
    .set { consensus_element_counts_ch }

Channel
    .of(['WT_D7_p1', 'WT_D11_p1'],
        ['WT_D7_p2', 'WT_D11_p2'],
        ['WT_D7_pM', 'WT_D11_pM'],
        ['WT_D11_p1', 'MUT_D11_p1'],
        ['WT_D11_p2', 'MUT_D11_p2'],
        ['WT_D11_pM', 'MUT_D11_pM'])
    .set { conditions_to_compare }

workflow {

    SELECT_SAMPLES( consensus_element_counts_ch,
                    conditions_to_compare )
}