Simplify and improve tests with usage of nft-utils 0.0.7

.github/workflows/validation.yml

@@ -9,7 +9,6 @@ on:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   NFT_VER: "0.9.3"
-  NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -49,13 +48,14 @@ jobs:
         uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3
         with:
           auto-update-conda: true
-          channels: conda-forge, bioconda
-          channel-priority: strict
           conda-remove-defaults: true
 
       - name: Clean workspace
         run: make clean
 
+      - name: Set NFT_WORKDIR dynamically
+        run: echo "NFT_WORKDIR=$HOME" >> $GITHUB_ENV
+
       - name: Build and validate plugin
         run: make validate
 

Makefile

@@ -31,4 +31,8 @@ release:
 # Run E2E validation test
 validate:
 	@$(MAKE) install
-	cd validation && nf-test test
+	cd validation && nf-test test --verbose --debug
+
+update-snapshots:
+	@$(MAKE) install
+	cd validation && nf-test test --verbose --debug --update-snapshot --clean-snapshot

validation/config-validation/error-test.nf.test

@@ -15,21 +15,8 @@ nextflow_pipeline {
         then {
             assert workflow.failed
 
-            // Should contain error message without color codes
-            assert workflow.stdout.any { it.contains("Pipeline is starting") }
-
-            // Check stdout for the actual error message (error appears in stdout in nf-test)
-            def errorMessage = workflow.stdout.join('\n')
-            assert errorMessage.contains("trailing comma")
-            assert errorMessage.contains("ERROR")
-            assert errorMessage.contains("HINT")
-
-            // Should NOT contain ANSI color codes
-            assert !errorMessage.contains('\033[')
-
-            // Snapshot monochrome error output
             assert snapshot(
-                workflow.stdout.findAll { it.contains("ERROR") || it.contains("HINT") }
+                filterNextflowOutput(workflow.stdout + workflow.stderr, keepAnsi: true)
             ).match()
         }
     }
@@ -45,22 +32,8 @@ nextflow_pipeline {
         then {
             assert workflow.failed
 
-            // Should contain error message with color codes
-            assert workflow.stdout.any { it.contains("Pipeline is starting") }
-
-            // Check stdout for the actual error message (error appears in stdout in nf-test)
-            def errorMessage = workflow.stdout.join('\n')
-            assert errorMessage.contains("trailing comma")
-            assert errorMessage.contains("ERROR")
-            assert errorMessage.contains("HINT")
-
-            // Note: Color codes may not be visible in test output due to nf-test capturing
-            // The important thing is that the function accepts the parameter without errors
-            // In real usage, colors would be displayed based on terminal capabilities
-
-            // Snapshot color error output
             assert snapshot(
-                workflow.stdout.findAll { it.contains("ERROR") || it.contains("HINT") }
+                filterNextflowOutput(workflow.stdout + workflow.stderr, keepAnsi: true)
             ).match()
         }
     }

validation/config-validation/error-test.nf.test.snap

@@ -2,27 +2,47 @@
     "Error output - Monochrome": {
         "content": [
             [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/config-validation/../config-validation/error-test.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "Pipeline is starting! \ud83d\ude80",
+                "==========================================",
+                "Color Formatting Error Test",
+                "==========================================",
+                "Testing profile with trailing comma (expected to fail)",
+                "Pipeline complete! \ud83d\udc4b",
+                "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, [CONTAINER]`.",
+                " -- Check script '[PATH]/config-validation/error-test.nf' at line: 24 or see '[PATH]/tests/[NFT_HASH]/meta/nextflow.log' file for more details",
                 "ERROR ~ ERROR ~ The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!",
-                "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`."
+                "WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info."
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-01T18:53:13.431098377"
+        "timestamp": "2025-10-29T09:37:52.569185136"
     },
     "Error output - Color": {
         "content": [
             [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/config-validation/../config-validation/error-test.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "Pipeline is starting! \ud83d\ude80",
+                "==========================================",
+                "Color Formatting Error Test",
+                "==========================================",
+                "Testing profile with trailing comma (expected to fail)",
+                "Pipeline complete! \ud83d\udc4b",
+                "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, [CONTAINER]`.",
+                " -- Check script '[PATH]/config-validation/error-test.nf' at line: 24 or see '[PATH]/tests/[NFT_HASH]/meta/nextflow.log' file for more details",
                 "ERROR ~ ERROR ~ The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!",
-                "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`."
+                "WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info."
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-01T18:53:15.822989509"
+        "timestamp": "2025-10-29T09:37:55.704620501"
     }
 }

validation/config-validation/main.nf.test

@@ -4,6 +4,16 @@ nextflow_pipeline {
     script "../config-validation/main.nf"
     config "../config-validation/nextflow.config"
 
+    test("Validate configuration functions") {
+
+        then {
+            assert workflow.success
+            assert snapshot(
+                filterNextflowOutput(workflow.stdout + workflow.stderr, keepAnsi: true)
+            ).match()
+        }
+    }
+
     test("monochrome_logs params enabled") {
 
         when {
@@ -14,12 +24,9 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-
-            // Should complete successfully (the detailed logs are not captured in workflow.stdout by nf-test)
-            assert workflow.stdout.any { it.contains("Pipeline is starting") }
-            assert workflow.stdout.any { it.contains("Pipeline complete") }
-
-            // Snapshot basic successful execution
+            assert snapshot(
+                filterNextflowOutput(workflow.stdout + workflow.stderr, keepAnsi: true)
+            ).match()
         }
     }
 
@@ -33,12 +40,9 @@ nextflow_pipeline {
 
         then {
             assert workflow.success
-
-            // Should complete successfully
-            assert workflow.stdout.any { it.contains("Pipeline is starting") }
-            assert workflow.stdout.any { it.contains("Pipeline complete") }
-
-            // Snapshot integration scenario success
+            assert snapshot(
+                filterNextflowOutput(workflow.stdout + workflow.stderr, keepAnsi: true)
+            ).match()
         }
     }
 }

validation/config-validation/main.nf.test.snap

@@ -0,0 +1,188 @@
+{
+    "Validate configuration functions": {
+        "content": [
+            [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/config-validation/../config-validation/main.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "Pipeline is starting! \ud83d\ude80",
+                "==========================================",
+                "Configuration Validation Test",
+                "==========================================",
+                "=== Testing checkConfigProvided() function ===",
+                "Configuration check result: false",
+                "\u2705 checkConfigProvided() executed successfully",
+                "=== Testing checkProfileProvided() function ===",
+                "Testing args 1: [[nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, test,[CONTAINER]]]",
+                "\u2705 Profile check completed for case 1",
+                "Testing args 2: [[nextflow, run, main.nf], [nextflow, run, main.nf, -other-param]]",
+                "\u2705 Profile check completed for case 2",
+                "Testing args 3: [[nextflow, run, main.nf, -profile], [-profile, [CONTAINER]]]",
+                "\u2705 Profile check completed for case 3",
+                "=== Testing color formatting feature ===",
+                "Testing monochrome output (default)",
+                "\u2705 Monochrome mode test completed",
+                "Testing color-enabled output",
+                "\u2705 Color-enabled mode test completed",
+                "Testing color formatting feature with valid profiles only",
+                "\u2705 Color formatting tests completed successfully",
+                "=== Testing checkCondaChannels() function ===",
+                "Conda channels check result: true",
+                "\u2705 checkCondaChannels() executed successfully",
+                "\u2705 Conda channels are configured correctly",
+                "=== Testing integration scenario ===",
+                "Simulating fetchngs pipeline initialization sequence...",
+                "Conda channels status: OK",
+                "Configuration status: May need custom config",
+                "Profile validation: Completed for typical fetchngs usage with color setting: monochrome",
+                "\u2705 Integration scenario completed successfully",
+                "=== Testing edge cases ===",
+                "\u2705 Empty arguments handled correctly",
+                "==========================================",
+                "Configuration Validation Complete",
+                "==========================================",
+                "Configuration Validation Results",
+                "==========================================",
+                "\u2705 checkConfigProvided() - Pipeline configuration validation tested",
+                "\u2705 checkProfileProvided() - Execution profile validation tested",
+                "\u2705 Color formatting - Both monochrome and color modes tested",
+                "\u2705 Error messages - Color formatting in error conditions tested",
+                "\u2705 checkCondaChannels() - Conda channel validation tested",
+                "\u2705 Integration scenario - Typical pipeline initialization flow tested",
+                "\u2705 Edge cases - Error handling and boundary conditions tested",
+                "Configuration validation functions ready for fetchngs! \ud83d\ude80",
+                "==========================================",
+                "Pipeline complete! \ud83d\udc4b",
+                "WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T09:40:48.846081851"
+    },
+    "monochrome_logs params disabled": {
+        "content": [
+            [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/config-validation/../config-validation/main.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "Pipeline is starting! \ud83d\ude80",
+                "==========================================",
+                "Configuration Validation Test",
+                "==========================================",
+                "=== Testing checkConfigProvided() function ===",
+                "Configuration check result: false",
+                "\u2705 checkConfigProvided() executed successfully",
+                "=== Testing checkProfileProvided() function ===",
+                "Testing args 1: [[nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, test,[CONTAINER]]]",
+                "\u2705 Profile check completed for case 1",
+                "Testing args 2: [[nextflow, run, main.nf], [nextflow, run, main.nf, -other-param]]",
+                "\u2705 Profile check completed for case 2",
+                "Testing args 3: [[nextflow, run, main.nf, -profile], [-profile, [CONTAINER]]]",
+                "\u2705 Profile check completed for case 3",
+                "=== Testing color formatting feature ===",
+                "Testing monochrome output (default)",
+                "\u2705 Monochrome mode test completed",
+                "Testing color-enabled output",
+                "\u2705 Color-enabled mode test completed",
+                "Testing color formatting feature with valid profiles only",
+                "\u2705 Color formatting tests completed successfully",
+                "=== Testing checkCondaChannels() function ===",
+                "Conda channels check result: true",
+                "\u2705 checkCondaChannels() executed successfully",
+                "\u2705 Conda channels are configured correctly",
+                "=== Testing integration scenario ===",
+                "Simulating fetchngs pipeline initialization sequence...",
+                "Conda channels status: OK",
+                "Configuration status: May need custom config",
+                "Profile validation: Completed for typical fetchngs usage with color setting: monochrome",
+                "\u2705 Integration scenario completed successfully",
+                "=== Testing edge cases ===",
+                "\u2705 Empty arguments handled correctly",
+                "==========================================",
+                "Configuration Validation Complete",
+                "==========================================",
+                "Configuration Validation Results",
+                "==========================================",
+                "\u2705 checkConfigProvided() - Pipeline configuration validation tested",
+                "\u2705 checkProfileProvided() - Execution profile validation tested",
+                "\u2705 Color formatting - Both monochrome and color modes tested",
+                "\u2705 Error messages - Color formatting in error conditions tested",
+                "\u2705 checkCondaChannels() - Conda channel validation tested",
+                "\u2705 Integration scenario - Typical pipeline initialization flow tested",
+                "\u2705 Edge cases - Error handling and boundary conditions tested",
+                "Configuration validation functions ready for fetchngs! \ud83d\ude80",
+                "==========================================",
+                "Pipeline complete! \ud83d\udc4b",
+                "WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T09:40:56.018591664"
+    },
+    "monochrome_logs params enabled": {
+        "content": [
+            [
+                "N E X T F L O W  ~  version [VERSION]",
+                "Launching `[PATH]/config-validation/../config-validation/main.nf` [RUN_NAME] DSL2 - revision: [REVISION]",
+                "Pipeline is starting! \ud83d\ude80",
+                "==========================================",
+                "Configuration Validation Test",
+                "==========================================",
+                "=== Testing checkConfigProvided() function ===",
+                "Configuration check result: false",
+                "\u2705 checkConfigProvided() executed successfully",
+                "=== Testing checkProfileProvided() function ===",
+                "Testing args 1: [[nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, [CONTAINER]], [nextflow, run, main.nf, -profile, test,[CONTAINER]]]",
+                "\u2705 Profile check completed for case 1",
+                "Testing args 2: [[nextflow, run, main.nf], [nextflow, run, main.nf, -other-param]]",
+                "\u2705 Profile check completed for case 2",
+                "Testing args 3: [[nextflow, run, main.nf, -profile], [-profile, [CONTAINER]]]",
+                "\u2705 Profile check completed for case 3",
+                "=== Testing color formatting feature ===",
+                "Testing monochrome output (default)",
+                "\u2705 Monochrome mode test completed",
+                "Testing color-enabled output",
+                "\u2705 Color-enabled mode test completed",
+                "Testing color formatting feature with valid profiles only",
+                "\u2705 Color formatting tests completed successfully",
+                "=== Testing checkCondaChannels() function ===",
+                "Conda channels check result: true",
+                "\u2705 checkCondaChannels() executed successfully",
+                "\u2705 Conda channels are configured correctly",
+                "=== Testing integration scenario ===",
+                "Simulating fetchngs pipeline initialization sequence...",
+                "Conda channels status: OK",
+                "Configuration status: May need custom config",
+                "Profile validation: Completed for typical fetchngs usage with color setting: true",
+                "\u2705 Integration scenario completed successfully",
+                "=== Testing edge cases ===",
+                "\u2705 Empty arguments handled correctly",
+                "==========================================",
+                "Configuration Validation Complete",
+                "==========================================",
+                "Configuration Validation Results",
+                "==========================================",
+                "\u2705 checkConfigProvided() - Pipeline configuration validation tested",
+                "\u2705 checkProfileProvided() - Execution profile validation tested",
+                "\u2705 Color formatting - Both monochrome and color modes tested",
+                "\u2705 Error messages - Color formatting in error conditions tested",
+                "\u2705 checkCondaChannels() - Conda channel validation tested",
+                "\u2705 Integration scenario - Typical pipeline initialization flow tested",
+                "\u2705 Edge cases - Error handling and boundary conditions tested",
+                "Configuration validation functions ready for fetchngs! \ud83d\ude80",
+                "==========================================",
+                "Pipeline complete! \ud83d\udc4b",
+                "WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T09:40:52.50112494"
+    }
+}

validation/config-validation/nextflow.config

@@ -67,7 +67,7 @@ params {
 // Process configuration - simulate realistic setup
 process {
     // Use conda by default for testing conda channel validation
-    conda         = "${projectDir}/environment.yml"
+    conda         = "${projectDir}/mock-data/environment.yml"
 
     // Resource limits
     memory        = '1 GB'