[Luna] Add test for CLI parameter override of paramsheet values

Test verifies that CLI flags (--round_digits 5) correctly override
paramsheet values (round_digits: 3) when using --paramset.

Two test cases:
1. CLI override: --round_digits 5 should take precedence over paramsheet
2. No override: paramsheet value (3) should be used

This validates the desired parameter priority:
CLI flags > paramsheet > defaults

Related to issue nf-core#472 and PR nf-core#623.

Author: suzannejin

tests/test_cli_override_paramsheet.nf.test

@@ -0,0 +1,74 @@
+nextflow_pipeline {
+
+    name "Test CLI parameter override of paramsheet values"
+    script "../main.nf"
+    tag "cli_override"
+    tag "pipeline"
+
+    test("CLI flag overrides paramsheet - round_digits") {
+
+        when {
+            params {
+                outdir        = "$outputDir"
+                paramsheet    = "${projectDir}/conf/test_paramsheet.yaml"
+                paramset_name = "deseq2_rnaseq_gsea"
+                // Paramsheet sets round_digits: 3, but CLI should override to 5
+                round_digits  = 5
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Paramsheet value without CLI override - round_digits") {
+        // This test runs the same paramset but WITHOUT the CLI override
+        // to verify that the paramsheet value (3) is used by default
+
+        when {
+            params {
+                outdir        = "$outputDir"
+                paramsheet    = "${projectDir}/conf/test_paramsheet.yaml"
+                paramset_name = "deseq2_rnaseq_gsea"
+                // No round_digits override - should use paramsheet value of 3
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}