212 lines
8.1 KiB
Text
Generated
212 lines
8.1 KiB
Text
Generated
nextflow_process {
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name "Test Process FASTQC"
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script "../main.nf"
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process "FASTQC"
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tag "modules"
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tag "modules_nfcore"
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tag "fastqc"
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test("sarscov2 single-end [fastq]") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[ id: 'test', single_end:true ],
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[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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// 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.
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// looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
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// https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
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{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
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{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
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{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_single") }
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)
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}
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}
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test("sarscov2 paired-end [fastq]") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: 'test', single_end: false], // meta map
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[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
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{ assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
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{ assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
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{ assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
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{ assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_paired") }
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)
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}
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}
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test("sarscov2 interleaved [fastq]") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: 'test', single_end: false], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
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{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
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{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
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)
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}
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}
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test("sarscov2 paired-end [bam]") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: 'test', single_end: false], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
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{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
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{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_bam") }
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)
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}
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}
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test("sarscov2 multiple [fastq]") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[id: 'test', single_end: false], // meta map
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[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
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{ assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
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{ assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
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{ assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
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{ assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
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{ assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
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{ assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
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{ assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
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{ assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
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)
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}
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}
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test("sarscov2 custom_prefix") {
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when {
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process {
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"""
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input[0] = Channel.of([
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[ id:'mysample', single_end:true ], // meta map
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file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
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{ assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
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{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
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{ assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
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)
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}
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}
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test("sarscov2 single-end [fastq] - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = Channel.of([
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[ id: 'test', single_end:true ],
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[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
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])
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"""
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}
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}
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then {
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assertAll (
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{ assert process.success },
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{ assert snapshot(process.out.html.collect { file(it[1]).getName() } +
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process.out.zip.collect { file(it[1]).getName() } +
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process.out.versions ).match("fastqc_stub") }
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)
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}
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}
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}
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