Setup file

[edmundmiller]

Just a thought since these could get quite verbose. But now having second thoughts now that I'm seeing they're not pure "Nextflow".

  test("Should use process ABRICATE_RUN to generate input data") {

   setup "./setup.nf"

        when {
            process {
                """
                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
                """
            }
        }
// ...

setup.nf

        setup {
            
            run("ABRICATE_RUN") {
                script "../../run/main.nf"
                process {
                    """
                    input[0] =  Channel.fromList([
                        tuple([ id:'test1', single_end:false ], // meta map
                            file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
                        tuple([ id:'test2', single_end:false ],
                            file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
                    ])
                    """
                }
            }

        }