Replace switch with else-if in utils_nfcore_pipeline (#7168)

I also added some tests to check that the function works as expected.
nf-core · Dec 6, 2024 · 51ae540 · 51ae540
1 parent c33544d
commit 51ae540
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Showing 2 changed files with 57 additions and 15 deletions.
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -206,22 +206,20 @@ def logColours(monochrome_logs=true) {
 // Return a single report from an object that may be a Path or List
 //
 def getSingleReport(multiqc_reports) {
-    switch (multiqc_reports) {
-        case Path:
-            return multiqc_reports
-        case List:
-            switch (multiqc_reports.size()) {
-                case 0:
-                    log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
-                    return null
-                case 1:
-                    return multiqc_reports.first()
-                default:
-                    log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
-                    return multiqc_reports.first()
-            }
-        default:
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
             return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
+        }
+    } else {
+        return null
     }
 }
 

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -79,4 +79,48 @@ nextflow_function {
             )
         }
     }
+
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
+
+        when {
+            function {
+                """
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result.contains("test.tsv") }
+            )
+        }
+    }
+
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
+
+        when {
+            function {
+                """
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
+            )
+        }
+    }
 }