Add test case with no significant hits

for additive GWAS pipeline should success filtered tophits are empty
genepi · Dec 15, 2023 · 948f694 · 948f694
1 parent 55572eb
commit 948f694
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Showing 2 changed files with 53 additions and 2 deletions.
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -803,7 +803,7 @@ test("Should execute pipeline for binary trait with optional regenie params") {
                 rsids_filename                = "$projectDir/tests/input/pipeline/rsids.tsv.gz"
                 annotation_min_log10p         = 2
                 regenie_step2_optional        = "--maxCatLevels 3"
-            outdir                        = "$outputDir"
+                outdir                        = "$outputDir"
         }
     }
     then {
@@ -936,8 +936,36 @@ test("Should GWAS with chunking and optional step 1 param") {
         assert workflow.failed
         snapshot(workflow.trace).match()
     }
+
+    }
 
-}
 
+   test("Should execute GWAS with additive testig with no significant hits") {
+
+    when {
+
+            params {
+                project                       = "test-gwas-binary"
+                genotypes_prediction          = "$projectDir/tests/input/pipeline/example.{bim,bed,fam}"
+                genotypes_association         = "$projectDir/tests/input/pipeline/example.bgen"
+                genotypes_build               = 'hg19'
+                genotypes_imputed_format      = 'bgen'
+                phenotypes_filename           = "$projectDir/tests/input/pipeline/phenotype_bin.txt"
+                phenotypes_columns            = 'Y1,Y2'
+                phenotypes_binary_trait       = true
+                regenie_test                  = 'additive'
+                outdir                        = "$outputDir"
+                rsids_filename                = "$projectDir/tests/input/pipeline/rsids.tsv.gz"
+                annotation_min_log10p         = 100
+                regenie_step1_optional        = "--pThresh 0.01"
+                outdir                        = "$outputDir"
+        }
+    }
+
+    then {
+        assert workflow.success
+        assert snapshot(new File("$outputDir/results/tophits/Y1.regenie.filtered.gz"), new File("$outputDir/results/tophits/Y2.regenie.filtered.gz"), workflow.trace).match()
+    }
+   }
 
 }
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -11,6 +11,17 @@
         ],
         "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",
@@ -167,6 +178,18 @@
         ],
         "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",