#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { NANOLYSE } from '../../../software/nanolyse/main.nf' addParams( options: [suffix: 'clean'] )

process GET_NANOLYSE_FASTA {
    output:
    path "*fasta.gz", emit: fasta

    script:
    """
    wget https://github.com/wdecoster/nanolyse/raw/master/reference/lambda.fasta.gz
    """
}

workflow test_nanolyse {
    input = [ [ id:'test' ], // meta map
              [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)]
            ]

    GET_NANOLYSE_FASTA()
    NANOLYSE ( input, GET_NANOLYSE_FASTA.out.fasta )
}