From 40a2c777dc3267a58dadc3b8ace442716e4da378 Mon Sep 17 00:00:00 2001 From: "Fischer, David" Date: Wed, 29 Oct 2025 09:55:05 +0100 Subject: [PATCH 1/2] update snapshots --- .../kraken2/kraken2/tests/main.nf.test | 73 ++++++++++++++++++- .../kraken2/kraken2/tests/main.nf.test.snap | 66 +++++++++++++++++ 2 files changed, 138 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index c0843df29acf..fe6988750027 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -133,10 +133,81 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.report, - process.out.classified_reads_assignment, process.out.versions, ).match() }, + { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" }, + ) + } + } + + test("single_end - stub") { + + tag "stub" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file("dummy1", checkIfExists: false)] + ] + input[1] = file("dummy2", checkIfExists: false) + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" }, + ) + } + } + + test("paired_end - stub") { + + tag "stub" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file("dummy1", checkIfExists: false)] + ] + input[1] = file("dummy2", checkIfExists: false) + input[2] = true + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.report, + process.out.versions, + ).match() + }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.classified_1.fastq.gz" }, + { assert process.out.classified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.classified_2.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(0) + ==~ ".*/test.unclassified_1.fastq.gz" }, + { assert process.out.unclassified_reads_fastq.get(0).get(1).get(1) + ==~ ".*/test.unclassified_2.fastq.gz" }, ) } } diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap index b432f878fbec..a46416a4c021 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap @@ -20,6 +20,51 @@ }, "timestamp": "2024-04-04T18:47:03.745692" }, + "paired_end - stub": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-28T16:49:09.20809324" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-16T13:56:24.287200136" + }, "sarscov2 illumina paired end [fastq]": { "content": [ [ @@ -70,5 +115,26 @@ "nextflow": "23.10.1" }, "timestamp": "2024-04-04T18:47:22.459465" + }, + "single_end - stub": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-28T16:45:27.933027038" } } \ No newline at end of file From 4ce0f80be467adb73a5684d032224c21f8503d86 Mon Sep 17 00:00:00 2001 From: "Fischer, David" Date: Wed, 29 Oct 2025 10:59:39 +0100 Subject: [PATCH 2/2] fix sarscov2 illumina single end [fastq] + save_reads_assignment test --- .../kraken2/kraken2/tests/main.nf.test | 2 -- .../kraken2/kraken2/tests/main.nf.test.snap | 30 +++++++++++++------ 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test index fe6988750027..d6275cd99a33 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test @@ -136,8 +136,6 @@ nextflow_process { process.out.versions, ).match() }, - { assert process.out.classified_reads_fastq.get(0).get(1) ==~ ".*/test.classified.fastq.gz" }, - { assert process.out.unclassified_reads_fastq.get(0).get(1) ==~ ".*/test.unclassified.fastq.gz" }, ) } } diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap index 2d0c2e0867a2..7a9912d5f34e 100644 --- a/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap +++ b/modules/nf-core/kraken2/kraken2/tests/main.nf.test.snap @@ -15,10 +15,10 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-09-26T10:40:05.762965901" + "timestamp": "2025-10-29T10:39:33.16840511" }, "paired_end - stub": { "content": [ @@ -32,14 +32,14 @@ ] ], [ - "versions.yml:md5,79adf2ca1cfc625cb77e391b27142c43" + "versions.yml:md5,3f1efbca96594bcbd7759bd992f3ffda" ] ], "meta": { "nf-test": "0.9.3", "nextflow": "25.04.8" }, - "timestamp": "2025-10-28T16:49:09.20809324" + "timestamp": "2025-10-29T10:57:46.285333986" }, "sarscov2 custom_prefix - stub": { "content": [ @@ -97,13 +97,25 @@ "test.kraken2.report.txt:md5,4227755fe40478b8d7dc8634b489761e" ] ], + [ + "versions.yml:md5,3f1efbca96594bcbd7759bd992f3ffda" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-29T10:43:03.036466597" + }, + "single_end - stub": { + "content": [ [ [ { "id": "test", "single_end": true }, - "test.kraken2.classifiedreads.txt:md5,e7a90531f0d8d777316515c36fe4cae0" + "test.kraken2.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ @@ -111,9 +123,9 @@ ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" + "nf-test": "0.9.3", + "nextflow": "25.04.8" }, - "timestamp": "2025-09-26T10:40:19.91998338" + "timestamp": "2025-10-29T10:44:44.698158761" } } \ No newline at end of file