Added function for parameter validation

lib/Validation.groovy

@@ -0,0 +1,115 @@
+import groovy.json.JsonSlurper
+import groovy.util.logging.Log
+
+class Validation {
+
+    /*
+    * Function to loop over all parameters defined in schema and check
+    * whether the given paremeters adhere to the specificiations
+    */
+    private static void validateParameters(params, json_schema, log, workflow){
+
+        def json = new File(json_schema).text
+        def Map json_params = (Map) new JsonSlurper().parseText(json).get('definitions')
+        def specified_param_keys = params.keySet()
+        def nf_params = ['profile', 'config', 'c', 'C', 'syslog', 'd', 'dockerize', 
+                        'bg', 'h', 'log', 'quiet', 'q', 'v', 'version']
+        def valid_params = []
+        def expected_params = []
+        def blacklist  = ['hostnames'] // ignored parameters
+
+
+        // Loop over all parameters in schema and compare to given parameters
+        for (group in json_params){
+            for (p in group.value['properties']){
+                if (!blacklist.contains(p.key)){
+                    valid_params.push(validateParamPair(params[p.key], p, log))
+                    expected_params.push(p.key)
+                }
+            }
+        }
+
+        // Exit if any invalid params where found
+        if (valid_params.contains(false)){
+            System.exit(0)
+        }
+
+        // Check for nextflow core params and unexpected params
+        for (specified_param in specified_param_keys){
+            // nextflow params
+            if (nf_params.contains(specified_param)){
+                log.error "ERROR: You have overwritten the core Nextflow parameter -${specified_param} with --${specified_param}!"
+                System.exit(0)
+            }
+            // unexpected params
+            if (!expected_params.contains(specified_param)){
+                log.warn "Unexpected parameter specified: ${specified_param}"               
+            }
+
+        }
+
+    }
+
+
+
+    /*
+    * Compare a pair of params (schema, command line) and check whether 
+    * they are valid
+    */
+     private static boolean validateParamPair(given_param, json_param, log){
+        def param_type = json_param.value['type']
+        def valid_param = true
+        def required = json_param.value['required']
+        def param_enum = json_param.value['enum']
+        def param_pattern = json_param.value['pattern']
+
+        // Check only if required or parameter is given
+        if (required || given_param){
+            def given_param_class = given_param.getClass()
+
+                switch(param_type) {
+                    case 'string':
+                        // If pattern given, check that param adheres to it
+                        if (param_pattern){
+                            valid_param = given_param ==~ param_pattern
+                        } 
+                        // If enum given, check that param is within choices
+                        else if (param_enum){
+                            valid_param = param_enum.contains(given_param)
+                        }
+                        // else just check whether valid String
+                        else {
+                            valid_param = given_param_class == String
+                        } 
+                        break
+                    case 'boolean':
+                        if (given_param_class == Boolean){
+                            valid_param = true
+                        }
+                        else if (given_param){
+                            valid_param = true
+                        }
+                        break
+                    case 'integer':
+                        valid_param = given_param_class == Integer
+                        break
+                    case 'number':
+                        valid_param = given_param_class == BigDecimal
+                        break
+                }
+
+            if (!valid_param){
+                log.error "ERROR: Parameter ${json_param.key} is wrong type! Expected ${param_type}, found ${given_param_class}, ${given_param}"
+                if (param_enum){
+                    log.error "Must be one of: ${param_enum}"
+                }
+                if (param_pattern){
+                    log.error "Parameter must adhere to the following pattern: ${param_pattern}"
+                }
+            }
+
+        }
+        return valid_param
+     }
+
+}

main.nf

@@ -22,6 +22,10 @@ if (params.help) {
     exit 0
 }
 
+////////////////////////////////////////////////////
+/* --         VALIDATE PARAMETERS              -- */
+////////////////////////////////////////////////////
+Validation.validateParameters(params, json_schema, log, workflow)
 ////////////////////////////////////////////////////
 /* --         PRINT PARAMETER SUMMARY          -- */
 ////////////////////////////////////////////////////

nextflow.config

@@ -9,8 +9,8 @@
 params {
 
   // Workflow flags
-  genome = false
-  input = 'data/*R1.fastq.gz'
+  genome = ''
+  input = ''
   outdir = './results'
   publish_dir_mode = 'copy'
 
@@ -20,7 +20,7 @@ params {
   save_reference = false
   min_aln_length = 15
   star_ignore_sjdbgtf = false
-  seq_center = false
+  seq_center = ''
 
   // Trimming options
   save_trimmed = false
@@ -48,7 +48,7 @@ params {
   ribo_database_manifest = "$baseDir/assets/rrna-db-defaults.txt"
 
   //Output options
-  bigwig=false
+  bigwig = false
 
   //Clustering options
   min_cluster = 30
@@ -59,9 +59,9 @@ params {
 
   // Boilerplate options
   enable_conda = false
-  name = false
-  clusterOptions = false
-  multiqc_config = false
+  name = ''
+  clusterOptions = ''
+  multiqc_config = ''
   email = false
   email_on_fail = false
   max_multiqc_email_size = 25.MB
@@ -73,10 +73,10 @@ params {
   igenomes_ignore = false
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-  hostnames = false
-  config_profile_description = false
-  config_profile_contact = false
-  config_profile_url = false
+  hostnames = ''
+  config_profile_description = ''
+  config_profile_contact = ''
+  config_profile_url = ''
   skip_multiqc = false
 
   // Defaults only, expecting to be overwritten

nextflow_schema.json

@@ -334,6 +334,7 @@
                     "description": "File size limit when attaching MultiQC reports to summary emails.",
                     "default": "25.MB",
                     "fa_icon": "fas fa-file-upload",
+                    "pattern": "\\d+\\.?\\s*[KMGT]?B?",
                     "hidden": true,
                     "help_text": "If file generated by pipeline exceeds the threshold, it will not be attached."
                 },
@@ -392,6 +393,7 @@
                     "description": "Maximum amount of memory that can be requested for any single job.",
                     "default": "128.GB",
                     "fa_icon": "fas fa-memory",
+                    "pattern": "\\d+\\.?\\s*[KMGT]?B?",
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
                 },
@@ -401,6 +403,7 @@
                     "default": "240.h",
                     "fa_icon": "far fa-clock",
                     "hidden": true,
+                    "pattern": "\\d+\\.?\\s*[mhd]",
                     "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                 }
             }