phaseimpute/modules/nf-core/minimac4/compressref/tests/main.nf.test at 3251eaabed8ea65036466e19b13039571113ef13 · LouisLeNezet/phaseimpute · GitHub

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nextflow_process {

    name "Test Process MINIMAC4_COMPRESSREF"
    script "../main.nf"
    process "MINIMAC4_COMPRESSREF"

    tag "modules"
    tag "modules_nfcore"
    tag "minimac4"
    tag "minimac4/compressref"

    test("homo sapiens - vcf") {
        when {
            process {
                """
                input[0] = Channel.of([
                    [ id:'input', single_end:false ], // meta map
                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists: true),
                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists: true),
                ])
                """
            }
        }

        then {
            assertAll(
                { assert process.success },
                { assert snapshot(
                    process.out.msav.collect{ file(it[1]).name },
                    ["versions.yml": path(process.out.versions.get(0)).yaml]
                ).match() }
            )
        }

    }

    test("homo sapiens - vcf - stub") {

        options "-stub"

        when {
            process {
                """
                input[0] = Channel.of([
                    [ id:'input', single_end:false ], // meta map
                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists: true),
                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists: true),
                ])
                """
            }
        }

        then {
            assertAll(
                { assert process.success },
                { assert snapshot(
                    process.out.msav,
                    ["versions.yml": path(process.out.versions.get(0)).yaml]
                ).match() }
            )
        }

    }

}