nextflow_process {

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

    tag "modules"
    tag "modules_nfcore"
    tag "fastqc"

    test("sarscov2 single-end [fastq]") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [ id: 'test', single_end:true ],
                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },

            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039

            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_single") }
            )
        }
    }

    test("sarscov2 paired-end [fastq]") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [id: 'test', single_end: false], // meta map
                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },

            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_paired") }
            )
        }
    }

    test("sarscov2 interleaved [fastq]") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [id: 'test', single_end: false], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
                ])
            """
            }
        }

        then {
            assertAll (
            { assert process.success },

            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
            )
        }
    }

    test("sarscov2 paired-end [bam]") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [id: 'test', single_end: false], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },

            { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
            { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_bam") }
            )
        }
    }

    test("sarscov2 multiple [fastq]") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [id: 'test', single_end: false], // meta map
                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },

            { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
            { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
            { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
            { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
            { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
            { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
            { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
            { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
            { assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
            { assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
            { assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
            { assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
            )
        }
    }

    test("sarscov2 custom_prefix") {

        when {
            process {
                """
                input[0] = Channel.of([
                    [ id:'mysample', single_end:true ], // meta map
                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },

            { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
            { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
            { assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },

            { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
            )
        }
    }

    test("sarscov2 single-end [fastq] - stub") {

        options "-stub"

        when {
            process {
                """
                input[0] = Channel.of([
                    [ id: 'test', single_end:true ],
                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
                ])
                """
            }
        }

        then {
            assertAll (
            { assert process.success },
            { assert snapshot(process.out.html.collect { file(it[1]).getName() } +
                                process.out.zip.collect { file(it[1]).getName() } +
                                process.out.versions ).match("fastqc_stub") }
            )
        }
    }

}