Merge pull request #143 from awgymer/137-nf-validation-fails-when-num…

…ber-parameters-are-set-to-0

Don't remove numeric 0 values from validation

plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy

@@ -1026,7 +1026,7 @@ class SchemaValidator extends PluginExtensionPoint {
         def Map new_params = (Map) params.getClass().newInstance(params)
         for (p in params) {
             // remove anything evaluating to false
-            if (!p['value']) {
+            if (!p['value'] && p['value'] != 0) {
                 new_params.remove(p.key)
             }
             // Cast MemoryUnit to String

plugins/nf-validation/src/test/nextflow/validation/PluginExtensionMethodsTest.groovy

@@ -511,6 +511,57 @@ class PluginExtensionMethodsTest extends Dsl2Spec{
         !stdout
     }
 
+    def 'correct validation of numerics - 0' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_required_numerics.json').toAbsolutePath().toString()
+        def  SCRIPT_TEXT = """
+            params.monochrome_logs = true
+            params.input = 'src/testResources/correct.csv'
+            params.outdir = 'src/testResources/testDir'
+            params.integer = 0
+            params.number = 0
+            include { validateParameters } from 'plugin/nf-validation'
+            
+            validateParameters(parameters_schema: '$schema', monochrome_logs: params.monochrome_logs)
+        """
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        noExceptionThrown()
+        !stdout
+    }
+
+    def 'fail validation of numerics - null' () {
+        given:
+        def schema = Path.of('src/testResources/nextflow_schema_required_numerics.json').toAbsolutePath().toString()
+        def  SCRIPT_TEXT = """
+            params.monochrome_logs = true
+            params.input = 'src/testResources/correct.csv'
+            params.outdir = 'src/testResources/testDir'
+            include { validateParameters } from 'plugin/nf-validation'
+            
+            validateParameters(parameters_schema: '$schema', monochrome_logs: params.monochrome_logs)
+        """
+
+        when:
+        dsl_eval(SCRIPT_TEXT)
+        def stdout = capture
+                .toString()
+                .readLines()
+                .findResults {it.contains('WARN nextflow.validation.SchemaValidator') || it.startsWith('* --') ? it : null }
+
+        then:
+        def error = thrown(SchemaValidationException)
+        error.message == "The following invalid input values have been detected:\n\n* Missing required parameter: --integer\n* Missing required parameter: --number\n\n"
+        !stdout
+    }
+
     def 'correct validation of file-path-pattern - glob' () {
         given:
         def schema = Path.of('src/testResources/nextflow_schema_file_path_pattern.json').toAbsolutePath().toString()

plugins/nf-validation/src/testResources/nextflow_schema_required_numerics.json

@@ -0,0 +1,62 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/testpipeline/master/nextflow_schema.json",
+    "title": "nf-core/testpipeline pipeline parameters",
+    "description": "this is a test",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+            "required": ["input", "outdir"],
+            "properties": {
+                "input": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|json)$",
+                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/testpipeline/usage#samplesheet-input).",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                }
+            }
+        },
+        "numeric_options": {
+            "title": "Numeric pipeline options",
+            "type": "object",
+            "fa_icon": "fas fa-dna",
+            "description": "Numeric options to be tested",
+            "required": ["integer", "number"],
+            "properties": {
+                "integer": {
+                    "type": "integer",
+                    "description": "An integer parameter.",
+                    "fa_icon": "fas fa-users-cog",
+                    "help_text": "Integer value"
+                },
+                "number": {
+                    "type": "number",
+                    "description": "A number parameter.",
+                    "fa_icon": "fas fa-users-cog",
+                    "help_text": "Number value"
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        },
+        {
+            "$ref": "#/definitions/numeric_options"
+        }
+    ]
+}