From b91acd15ec1ada07a5a3702688fed218031473fa Mon Sep 17 00:00:00 2001 From: Lukas Forer Date: Sat, 25 May 2024 14:47:14 +0200 Subject: [PATCH] Cleanup obsolete snapshots and add missing snapshots --- tests/main.nf.test.snap | 194 +++++++++++++++--- .../modules/local/filter_results.nf.test.snap | 12 ++ .../modules/local/regenie_step1.nf.test.snap | 4 + .../modules/local/regenie_step2.nf.test.snap | 4 + 4 files changed, 191 insertions(+), 23 deletions(-) diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap index b0a3874e..4012da2a 100644 --- a/tests/main.nf.test.snap +++ b/tests/main.nf.test.snap @@ -9,19 +9,12 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:03:22.52629" }, - "Should fail(?) because no significant hit was found": { - "content": [ - "Y1.regenie.gz:md5,f80dee2e3a0f824408cfa0bf963f4a2d", - { - "tasksFailed": 0, - "tasksCount": 14, - "tasksSucceeded": 14 - } - ], - "timestamp": "2023-12-15T11:12:53.355508" - }, "Should execute GWAS with phenotype file in tabs format": { "content": [ "Y1.regenie.gz:md5,3b46e913e302d59a27c87f989384a689", @@ -32,6 +25,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:02:25.833032" }, "Should execute GWAS with binary trait (with missing data)": { @@ -44,6 +41,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:42:46.245326" }, "Should execute GWAS with liftover to hg38 and annotation": { @@ -56,6 +57,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:48:11.2585" }, "Should execute GWAS with custom Manhattan plot y-limit": { @@ -68,6 +73,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:01:57.60339" }, "Should execute pipeline for binary trait with optional regenie step1 param": { @@ -80,6 +89,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:05:12.14642" }, "Should execute gene-based test pipeline with specified parameters with sum": { @@ -92,6 +105,10 @@ "tasksSucceeded": 12 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2024-01-30T13:03:21.803945401" }, "Should execute GWAS with skipped predictions": { @@ -104,6 +121,10 @@ "tasksSucceeded": 12 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:04:16.854487" }, "Should execute liftover and GWAS pipeline": { @@ -116,6 +137,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:40:00.93939" }, "Should execute GWAS with header in phenotype file with chunking": { @@ -128,6 +153,10 @@ "tasksSucceeded": 34 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:56:14.80547" }, "Should execute GWAS with force step 1": { @@ -140,6 +169,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:47:14.573846" }, "Should execute GWAS with additive test and multiple chromosomes": { @@ -152,6 +185,10 @@ "tasksSucceeded": 18 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:39:07.072853" }, "Should execute GWAS with pruning pipeline": { @@ -164,6 +201,10 @@ "tasksSucceeded": 16 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:31:33.574586" }, "Should execute GWAS with binary trait (no Firth approximation)": { @@ -176,20 +217,12 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:41:52.068742" }, - "Should execute GWAS with additive testig with no significant hits": { - "content": [ - "Y1.regenie.filtered.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - "Y2.regenie.filtered.gz:md5,d41d8cd98f00b204e9800998ecf8427e", - { - "tasksFailed": 0, - "tasksCount": 14, - "tasksSucceeded": 14 - } - ], - "timestamp": "2023-12-15T11:19:19.183957" - }, "Should execute GWAS with header in phenotype file (custom batch size)": { "content": [ "PHENO1.regenie.gz:md5,c03c47e1d4300277f2a445afc14c6d1e", @@ -200,6 +233,10 @@ "tasksSucceeded": 40 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-15T09:39:33.247657" }, "Should GWAS with chunking and optional step 1 param": { @@ -212,6 +249,10 @@ "tasksSucceeded": 40 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2024-01-30T14:58:51.832310272" }, "Should execute GWAS with recessive test": { @@ -224,6 +265,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:03:50.532327" }, "Should execute GWAS with header in phenotype file": { @@ -236,6 +281,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:00:13.784558" }, "Should execute GWAS with additive test on 2 chromosomes": { @@ -248,6 +297,10 @@ "tasksSucceeded": 19 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:43:15.539844" }, "Should execute GWAS with header in phenotype file (default batch size)": { @@ -260,6 +313,10 @@ "tasksSucceeded": 34 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:57:23.850687" }, "Should execute GWAS with additive test and RSIDs": { @@ -272,8 +329,43 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:40:28.618801" }, + "Should execute pipeline applying an additive model": { + "content": [ + "Y1.regenie.gz:md5,3b46e913e302d59a27c87f989384a689", + { + "tasksFailed": 0, + "tasksCount": 15, + "tasksSucceeded": 15 + } + ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-14T15:01:58.151408" + }, + "Should execute GWAS with phenotype file containing three empty values": { + "content": [ + "Y1.regenie.gz:md5,3b46e913e302d59a27c87f989384a689", + "Y2.regenie.gz:md5,d9cb8506e0819ddff02eb1122284f9f3", + { + "tasksFailed": 0, + "tasksCount": 15, + "tasksSucceeded": 15 + } + ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-14T15:17:10.622828" + }, "Should execute GWAS with dominant test": { "content": [ "Y1.regenie.gz:md5,2b35ee6a9e801d5f8ffe65f5d3af6331", @@ -284,6 +376,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:46:46.732441" }, "Should execute GWAS with interaction tests (interaction term)": { @@ -296,6 +392,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:48:57.716231" }, "Should execute gene-based test pipeline": { @@ -308,6 +408,10 @@ "tasksSucceeded": 12 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2024-01-30T13:04:14.539623588" }, "Should execute pipeline for binary trait": { @@ -320,6 +424,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:41:24.903565" }, "Should execute GWAS with binary trait (no Firth)": { @@ -332,6 +440,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:42:19.084491" }, "Should fail since no phenotype is specified": { @@ -342,6 +454,10 @@ "tasksSucceeded": 0 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-15T09:46:31.396474" }, "Should execute GWAS with additive testing with no significant hits": { @@ -354,6 +470,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2024-01-30T13:00:05.31347319" }, "Should execute liftover and GWAS pipeline with array results": { @@ -366,6 +486,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:39:34.107772" }, "Should execute gene-based-test with only one output file": { @@ -377,6 +501,10 @@ "tasksSucceeded": 10 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2024-01-30T13:41:43.043614115" }, "Should execute GWAS with deletion of missing phenotype data": { @@ -389,6 +517,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:46:18.588273" }, "Should execute GWAS with interaction tests": { @@ -401,6 +533,10 @@ "tasksSucceeded": 15 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:48:34.843303" }, "Should execute pipeline for binary trait with optional regenie params": { @@ -413,6 +549,10 @@ "tasksSucceeded": 14 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T17:04:44.409121" }, "Should execute GWAS with condition file": { @@ -425,6 +565,10 @@ "tasksSucceeded": 16 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:45:21.791936" }, "Should execute GWAS with covariates file": { @@ -437,6 +581,10 @@ "tasksSucceeded": 16 } ], + "meta": { + "nf-test": "0.8.5", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T16:45:50.402989" } } \ No newline at end of file diff --git a/tests/modules/local/filter_results.nf.test.snap b/tests/modules/local/filter_results.nf.test.snap index 6eb1e2be..8e25aed0 100644 --- a/tests/modules/local/filter_results.nf.test.snap +++ b/tests/modules/local/filter_results.nf.test.snap @@ -24,6 +24,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-15T10:30:54.852916" }, "Should output only 117 filtered lines": { @@ -51,6 +55,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-15T10:16:52.606586" }, "Should output an empty file": { @@ -78,6 +86,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-15T10:37:15.316506" } } \ No newline at end of file diff --git a/tests/modules/local/regenie_step1.nf.test.snap b/tests/modules/local/regenie_step1.nf.test.snap index c8d4e77a..a7adacde 100644 --- a/tests/modules/local/regenie_step1.nf.test.snap +++ b/tests/modules/local/regenie_step1.nf.test.snap @@ -4,6 +4,10 @@ "regenie_step1_out_1.loco.gz:md5,5e3f3bd230d519c0740ae158d2ba2f41", "regenie_step1_out_2.loco.gz:md5,ff2327b54520a6885df85ad27cebcd19" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T15:05:10.807967" } } \ No newline at end of file diff --git a/tests/modules/local/regenie_step2.nf.test.snap b/tests/modules/local/regenie_step2.nf.test.snap index c1c0b7b4..2c3dc7e7 100644 --- a/tests/modules/local/regenie_step2.nf.test.snap +++ b/tests/modules/local/regenie_step2.nf.test.snap @@ -7,6 +7,10 @@ "example.regenie.Ydict:md5,89086862ab0ea9b2a1a92f3bee0b55d3" ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, "timestamp": "2023-12-14T14:47:08.826254" } } \ No newline at end of file