Added groovy functions in lib to reduce boilerplate code

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/lib/Headers.groovy

@@ -0,0 +1,43 @@
+/*
+ * This file holds several functions used to render the nf-core ANSI header.
+ */
+
+class Headers {
+
+    private static Map log_colours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
+        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
+        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']      = monochrome_logs ? '' :  "\033[0;33m"
+        colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
+        colorcodes['red']         = monochrome_logs ? '' : "\033[1;91m"
+        return colorcodes
+    }
+
+    static String dashed_line(monochrome_logs) {
+        Map colors = log_colours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    static String nf_core(workflow, monochrome_logs) {
+        Map colors = log_colours(monochrome_logs)
+        String.format(
+            """\n
+            ${dashed_line(monochrome_logs)}
+                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${dashed_line(monochrome_logs)}
+            """.stripIndent()
+        )
+    }
+}

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/lib/NfcoreSchema.groovy

@@ -12,6 +12,7 @@ import groovy.json.JsonSlurper
 import groovy.json.JsonBuilder
 
 class NfcoreSchema {
+
     /*
     * Function to loop over all parameters defined in schema and check
     * whether the given paremeters adhere to the specificiations
@@ -134,23 +135,31 @@ class NfcoreSchema {
         try {
             schema.validate(paramsJSON)
         } catch (ValidationException e) {
-            println ""
+            println ''
             log.error 'ERROR: Validation of pipeline parameters failed!'
             JSONObject exceptionJSON = e.toJSON()
             printExceptions(exceptionJSON, paramsJSON, log)
-            if (unexpectedParams.size() > 0){
-                println ""
-                def warn_msg = 'Found unexpected parameters:'
-                for (unexpectedParam in unexpectedParams){
-                    warn_msg = warn_msg + "\n* --${unexpectedParam}: ${paramsJSON[unexpectedParam].toString()}"
-                }
-                log.warn warn_msg
-            }
-            println ""
+            println ''
             has_error = true
         }
 
-        if(has_error){
+        // Check for unexpected parameters
+        // Getting this message a lot for parameters that you *do* expect?
+        // You can make a csv list of expected params not in the schema with 'params.schema_ignore_params'
+        // for example, in your institutional config
+        if (unexpectedParams.size() > 0) {
+            Map colors = log_colours(params.monochrome_logs)
+            println ''
+            def warn_msg = 'Found unexpected parameters:'
+            for (unexpectedParam in unexpectedParams) {
+                warn_msg = warn_msg + "\n* --${unexpectedParam}: ${paramsJSON[unexpectedParam].toString()}"
+            }
+            log.warn warn_msg
+            log.info "- ${colors.dim}(Hide this message with 'params.schema_ignore_params')${colors.reset} -"
+            println ''
+        }
+
+        if (has_error) {
             System.exit(1)
         }
 
@@ -163,11 +172,11 @@ class NfcoreSchema {
         if (causingExceptions.length() == 0) {
             def m = exJSON['message'] =~ /required key \[([^\]]+)\] not found/
             // Missing required param
-            if(m.matches()){
+            if (m.matches()) {
                 log.error "* Missing required parameter: --${m[0][1]}"
             }
             // Other base-level error
-            else if(exJSON['pointerToViolation'] == '#'){
+            else if (exJSON['pointerToViolation'] == '#') {
                 log.error "* ${exJSON['message']}"
             }
             // Error with specific param
@@ -205,4 +214,222 @@ class NfcoreSchema {
         return new_params
     }
 
+     /*
+     * This method tries to read a JSON params file
+     */
+    private static LinkedHashMap params_load(String json_schema) {
+        def params_map = new LinkedHashMap()
+        try {
+            params_map = params_read(json_schema)
+        } catch (Exception e) {
+            println "Could not read parameters settings from JSON. $e"
+            params_map = new LinkedHashMap()
+        }
+        return params_map
+    }
+
+    private static Map log_colours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+        colorcodes['reset']       = monochrome_logs ? '' : "\033[0m"
+        colorcodes['dim']         = monochrome_logs ? '' : "\033[2m"
+        colorcodes['black']       = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['green']       = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']      = monochrome_logs ? '' :  "\033[0;33m"
+        colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['blue']        = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']      = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']        = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']       = monochrome_logs ? '' : "\033[0;37m"
+        colorcodes['red']         = monochrome_logs ? '' : "\033[1;91m"
+        return colorcodes
+    }
+
+    static String dashed_line(monochrome_logs) {
+        Map colors = log_colours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    /*
+    Method to actually read in JSON file using Groovy.
+    Group (as Key), values are all parameters
+        - Parameter1 as Key, Description as Value
+        - Parameter2 as Key, Description as Value
+        ....
+    Group
+        -
+    */
+    private static LinkedHashMap params_read(String json_schema) throws Exception {
+        def json = new File(json_schema).text
+        def Map json_params = (Map) new JsonSlurper().parseText(json).get('definitions')
+        /* Tree looks like this in nf-core schema
+         * definitions <- this is what the first get('definitions') gets us
+             group 1
+               title
+               description
+                 properties
+                   parameter 1
+                     type
+                     description
+                   parameter 2
+                     type
+                     description
+             group 2
+               title
+               description
+                 properties
+                   parameter 1
+                     type
+                     description
+        */
+        def params_map = new LinkedHashMap()
+        json_params.each { key, val ->
+            def Map group = json_params."$key".properties // Gets the property object of the group
+            def title = json_params."$key".title
+            def sub_params = new LinkedHashMap()
+            group.each { innerkey, value ->
+                sub_params.put(innerkey, value)
+            }
+            params_map.put(title, sub_params)
+        }
+        return params_map
+    }
+
+    /*
+     * Get maximum number of characters across all parameter names
+     */
+    private static Integer params_max_chars(params_map) {
+        Integer max_chars = 0
+        for (group in params_map.keySet()) {
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            for (param in group_params.keySet()) {
+                if (param.size() > max_chars) {
+                    max_chars = param.size()
+                }
+            }
+        }
+        return max_chars
+    }
+
+    /*
+     * Beautify parameters for --help
+     */
+    private static String params_help(workflow, params, json_schema, command) {
+        String output  = ''
+        output        += 'Typical pipeline command:\n\n'
+        output        += "    ${command}\n\n"
+        def params_map = params_load(json_schema)
+        def max_chars  = params_max_chars(params_map) + 1
+        for (group in params_map.keySet()) {
+            output += group + '\n'
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            for (param in group_params.keySet()) {
+                def type = '[' + group_params.get(param).type + ']'
+                def description = group_params.get(param).description
+                def defaultValue = group_params.get(param).default ? "  [default: " + group_params.get(param).default.toString() + "]" : ''
+                output += "    \u001B[1m--" +  param.padRight(max_chars) + "\u001B[1m" + type.padRight(10) + description + defaultValue + '\n'
+            }
+            output += '\n'
+        }
+        output += dashed_line(params.monochrome_logs)
+        output += '\n\n' + dashed_line(params.monochrome_logs)
+        return output
+    }
+
+    /*
+     * Groovy Map summarising parameters/workflow options used by the pipeline
+     */
+    private static LinkedHashMap params_summary_map(workflow, params, json_schema) {
+        // Get a selection of core Nextflow workflow options
+        def Map workflow_summary = [:]
+        if (workflow.revision) {
+            workflow_summary['revision'] = workflow.revision
+        }
+        workflow_summary['runName']      = workflow.runName
+        if (workflow.containerEngine) {
+            workflow_summary['containerEngine'] = "$workflow.containerEngine"
+        }
+        if (workflow.container) {
+            workflow_summary['container']       = "$workflow.container"
+        }
+        workflow_summary['launchDir']    = workflow.launchDir
+        workflow_summary['workDir']      = workflow.workDir
+        workflow_summary['projectDir']   = workflow.projectDir
+        workflow_summary['userName']     = workflow.userName
+        workflow_summary['profile']      = workflow.profile
+        workflow_summary['configFiles']  = workflow.configFiles.join(', ')
+
+        // Get pipeline parameters defined in JSON Schema
+        def Map params_summary = [:]
+        def blacklist  = ['hostnames']
+        def params_map = params_load(json_schema)
+        for (group in params_map.keySet()) {
+            def sub_params = new LinkedHashMap()
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            for (param in group_params.keySet()) {
+                if (params.containsKey(param) && !blacklist.contains(param)) {
+                    def params_value = params.get(param)
+                    def schema_value = group_params.get(param).default
+                    def param_type   = group_params.get(param).type
+                    if (schema_value == null) {
+                        if (param_type == 'boolean') {
+                            schema_value = false
+                        }
+                        if (param_type == 'string') {
+                            schema_value = ''
+                        }
+                        if (param_type == 'integer') {
+                            schema_value = 0
+                        }
+                    } else {
+                        if (param_type == 'string') {
+                            if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
+                                def sub_string = schema_value.replace('\$projectDir', '')
+                                sub_string     = sub_string.replace('\${projectDir}', '')
+                                if (params_value.contains(sub_string)) {
+                                    schema_value = params_value
+                                }
+                            }
+                            if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
+                                def sub_string = schema_value.replace('\$params.outdir', '')
+                                sub_string     = sub_string.replace('\${params.outdir}', '')
+                                if ("${params.outdir}${sub_string}" == params_value) {
+                                    schema_value = params_value
+                                }
+                            }
+                        }
+                    }
+
+                    if (params_value != schema_value) {
+                        sub_params.put("$param", params_value)
+                    }
+                }
+            }
+            params_summary.put(group, sub_params)
+        }
+        return [ 'Core Nextflow options' : workflow_summary ] << params_summary
+    }
+
+    /*
+     * Beautify parameters for summary and return as string
+     */
+    private static String params_summary_log(workflow, params, json_schema) {
+        String output  = ''
+        def params_map = params_summary_map(workflow, params, json_schema)
+        def max_chars  = params_max_chars(params_map)
+        for (group in params_map.keySet()) {
+            def group_params = params_map.get(group)  // This gets the parameters of that particular group
+            if (group_params) {
+                output += group + '\n'
+                for (param in group_params.keySet()) {
+                    output += "    \u001B[1m" +  param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + '\n'
+                }
+                output += '\n'
+            }
+        }
+        output += "[Only displaying parameters that differ from pipeline default]\n"
+        output += dashed_line(params.monochrome_logs)
+        output += '\n\n' + dashed_line(params.monochrome_logs)
+        return output
+    }
+
 }