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529 lines
22 KiB
Groovy
529 lines
22 KiB
Groovy
//
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// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
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//
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import org.everit.json.schema.Schema
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import org.everit.json.schema.loader.SchemaLoader
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import org.everit.json.schema.ValidationException
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import org.json.JSONObject
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import org.json.JSONTokener
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import org.json.JSONArray
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import groovy.json.JsonSlurper
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import groovy.json.JsonBuilder
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class NfcoreSchema {
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//
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// Resolve Schema path relative to main workflow directory
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//
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public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
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return "${workflow.projectDir}/${schema_filename}"
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}
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//
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// Function to loop over all parameters defined in schema and check
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// whether the given parameters adhere to the specifications
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//
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/* groovylint-disable-next-line UnusedPrivateMethodParameter */
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public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
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def has_error = false
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//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
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// Check for nextflow core params and unexpected params
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def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
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def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
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def nf_params = [
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// Options for base `nextflow` command
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'bg',
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'c',
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'C',
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'config',
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'd',
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'D',
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'dockerize',
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'h',
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'log',
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'q',
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'quiet',
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'syslog',
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'v',
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// Options for `nextflow run` command
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'ansi',
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'ansi-log',
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'bg',
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'bucket-dir',
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'c',
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'cache',
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'config',
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'dsl2',
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'dump-channels',
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'dump-hashes',
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'E',
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'entry',
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'latest',
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'lib',
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'main-script',
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'N',
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'name',
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'offline',
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'params-file',
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'pi',
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'plugins',
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'poll-interval',
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'pool-size',
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'profile',
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'ps',
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'qs',
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'queue-size',
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'r',
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'resume',
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'revision',
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'stdin',
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'stub',
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'stub-run',
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'test',
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'w',
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'with-charliecloud',
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'with-conda',
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'with-dag',
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'with-docker',
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'with-mpi',
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'with-notification',
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'with-podman',
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'with-report',
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'with-singularity',
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'with-timeline',
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'with-tower',
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'with-trace',
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'with-weblog',
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'without-docker',
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'without-podman',
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'work-dir'
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]
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def unexpectedParams = []
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// Collect expected parameters from the schema
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def expectedParams = []
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def enums = [:]
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for (group in schemaParams) {
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for (p in group.value['properties']) {
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expectedParams.push(p.key)
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if (group.value['properties'][p.key].containsKey('enum')) {
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enums[p.key] = group.value['properties'][p.key]['enum']
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}
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}
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}
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for (specifiedParam in params.keySet()) {
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// nextflow params
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if (nf_params.contains(specifiedParam)) {
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log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
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has_error = true
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}
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// unexpected params
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def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
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def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
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def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
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def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
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if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
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// Temporarily remove camelCase/camel-case params #1035
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def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
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if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
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unexpectedParams.push(specifiedParam)
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}
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}
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}
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//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
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// Validate parameters against the schema
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InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
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JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
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// Remove anything that's in params.schema_ignore_params
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raw_schema = removeIgnoredParams(raw_schema, params)
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Schema schema = SchemaLoader.load(raw_schema)
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// Clean the parameters
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def cleanedParams = cleanParameters(params)
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// Convert to JSONObject
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def jsonParams = new JsonBuilder(cleanedParams)
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JSONObject params_json = new JSONObject(jsonParams.toString())
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// Validate
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try {
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schema.validate(params_json)
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} catch (ValidationException e) {
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println ''
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log.error 'ERROR: Validation of pipeline parameters failed!'
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JSONObject exceptionJSON = e.toJSON()
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printExceptions(exceptionJSON, params_json, log, enums)
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println ''
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has_error = true
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}
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// Check for unexpected parameters
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if (unexpectedParams.size() > 0) {
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Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
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println ''
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def warn_msg = 'Found unexpected parameters:'
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for (unexpectedParam in unexpectedParams) {
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warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
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}
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log.warn warn_msg
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log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
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println ''
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}
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if (has_error) {
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System.exit(1)
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}
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}
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//
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// Beautify parameters for --help
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//
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public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
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Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
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Integer num_hidden = 0
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String output = ''
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output += 'Typical pipeline command:\n\n'
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output += " ${colors.cyan}${command}${colors.reset}\n\n"
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Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
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Integer max_chars = paramsMaxChars(params_map) + 1
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Integer desc_indent = max_chars + 14
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Integer dec_linewidth = 160 - desc_indent
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for (group in params_map.keySet()) {
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Integer num_params = 0
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String group_output = colors.underlined + colors.bold + group + colors.reset + '\n'
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def group_params = params_map.get(group) // This gets the parameters of that particular group
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for (param in group_params.keySet()) {
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if (group_params.get(param).hidden && !params.show_hidden_params) {
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num_hidden += 1
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continue;
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}
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def type = '[' + group_params.get(param).type + ']'
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def description = group_params.get(param).description
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def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : ''
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def description_default = description + colors.dim + defaultValue + colors.reset
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// Wrap long description texts
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// Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap
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if (description_default.length() > dec_linewidth){
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List olines = []
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String oline = "" // " " * indent
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description_default.split(" ").each() { wrd ->
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if ((oline.size() + wrd.size()) <= dec_linewidth) {
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oline += wrd + " "
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} else {
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olines += oline
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oline = wrd + " "
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}
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}
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olines += oline
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description_default = olines.join("\n" + " " * desc_indent)
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}
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group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n'
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num_params += 1
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}
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group_output += '\n'
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if (num_params > 0){
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output += group_output
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}
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}
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if (num_hidden > 0){
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output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
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}
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output += NfcoreTemplate.dashedLine(params.monochrome_logs)
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return output
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}
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//
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// Groovy Map summarising parameters/workflow options used by the pipeline
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//
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public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
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// Get a selection of core Nextflow workflow options
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def Map workflow_summary = [:]
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if (workflow.revision) {
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workflow_summary['revision'] = workflow.revision
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}
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workflow_summary['runName'] = workflow.runName
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if (workflow.containerEngine) {
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workflow_summary['containerEngine'] = workflow.containerEngine
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}
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if (workflow.container) {
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workflow_summary['container'] = workflow.container
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}
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workflow_summary['launchDir'] = workflow.launchDir
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workflow_summary['workDir'] = workflow.workDir
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workflow_summary['projectDir'] = workflow.projectDir
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workflow_summary['userName'] = workflow.userName
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workflow_summary['profile'] = workflow.profile
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workflow_summary['configFiles'] = workflow.configFiles.join(', ')
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// Get pipeline parameters defined in JSON Schema
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def Map params_summary = [:]
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def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
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for (group in params_map.keySet()) {
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def sub_params = new LinkedHashMap()
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def group_params = params_map.get(group) // This gets the parameters of that particular group
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for (param in group_params.keySet()) {
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if (params.containsKey(param)) {
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def params_value = params.get(param)
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def schema_value = group_params.get(param).default
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def param_type = group_params.get(param).type
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if (schema_value != null) {
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if (param_type == 'string') {
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if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
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def sub_string = schema_value.replace('\$projectDir', '')
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sub_string = sub_string.replace('\${projectDir}', '')
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if (params_value.contains(sub_string)) {
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schema_value = params_value
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}
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}
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if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
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def sub_string = schema_value.replace('\$params.outdir', '')
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sub_string = sub_string.replace('\${params.outdir}', '')
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if ("${params.outdir}${sub_string}" == params_value) {
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schema_value = params_value
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}
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}
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}
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}
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// We have a default in the schema, and this isn't it
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if (schema_value != null && params_value != schema_value) {
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sub_params.put(param, params_value)
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}
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// No default in the schema, and this isn't empty
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else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
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sub_params.put(param, params_value)
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}
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}
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}
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params_summary.put(group, sub_params)
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}
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return [ 'Core Nextflow options' : workflow_summary ] << params_summary
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}
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//
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// Beautify parameters for summary and return as string
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//
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public static String paramsSummaryLog(workflow, params) {
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Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
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String output = ''
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def params_map = paramsSummaryMap(workflow, params)
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def max_chars = paramsMaxChars(params_map)
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for (group in params_map.keySet()) {
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def group_params = params_map.get(group) // This gets the parameters of that particular group
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if (group_params) {
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output += colors.bold + group + colors.reset + '\n'
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for (param in group_params.keySet()) {
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output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n'
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}
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output += '\n'
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}
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}
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output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
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output += NfcoreTemplate.dashedLine(params.monochrome_logs)
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return output
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}
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//
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// Loop over nested exceptions and print the causingException
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//
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private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
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def causingExceptions = ex_json['causingExceptions']
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if (causingExceptions.length() == 0) {
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def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
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// Missing required param
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if (m.matches()) {
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log.error "* Missing required parameter: --${m[0][1]}"
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}
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// Other base-level error
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else if (ex_json['pointerToViolation'] == '#') {
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log.error "* ${ex_json['message']}"
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}
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// Error with specific param
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else {
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def param = ex_json['pointerToViolation'] - ~/^#\//
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def param_val = params_json[param].toString()
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if (enums.containsKey(param)) {
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def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
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if (enums[param].size() > limit) {
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log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
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} else {
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log.error "${error_msg}: ${enums[param].join(', ')})"
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}
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} else {
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log.error "* --${param}: ${ex_json['message']} (${param_val})"
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}
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}
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}
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for (ex in causingExceptions) {
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printExceptions(ex, params_json, log, enums)
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}
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}
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//
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// Remove an element from a JSONArray
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//
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private static JSONArray removeElement(json_array, element) {
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def list = []
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int len = json_array.length()
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for (int i=0;i<len;i++){
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list.add(json_array.get(i).toString())
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}
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list.remove(element)
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JSONArray jsArray = new JSONArray(list)
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return jsArray
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}
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//
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// Remove ignored parameters
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//
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private static JSONObject removeIgnoredParams(raw_schema, params) {
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// Remove anything that's in params.schema_ignore_params
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params.schema_ignore_params.split(',').each{ ignore_param ->
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if(raw_schema.keySet().contains('definitions')){
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raw_schema.definitions.each { definition ->
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for (key in definition.keySet()){
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if (definition[key].get("properties").keySet().contains(ignore_param)){
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// Remove the param to ignore
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definition[key].get("properties").remove(ignore_param)
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// If the param was required, change this
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if (definition[key].has("required")) {
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def cleaned_required = removeElement(definition[key].required, ignore_param)
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definition[key].put("required", cleaned_required)
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}
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}
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}
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}
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}
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if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
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raw_schema.get("properties").remove(ignore_param)
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}
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if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
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def cleaned_required = removeElement(raw_schema.required, ignore_param)
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raw_schema.put("required", cleaned_required)
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}
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}
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return raw_schema
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}
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//
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// Clean and check parameters relative to Nextflow native classes
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//
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private static Map cleanParameters(params) {
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def new_params = params.getClass().newInstance(params)
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for (p in params) {
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// remove anything evaluating to false
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if (!p['value']) {
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new_params.remove(p.key)
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}
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// Cast MemoryUnit to String
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if (p['value'].getClass() == nextflow.util.MemoryUnit) {
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new_params.replace(p.key, p['value'].toString())
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}
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// Cast Duration to String
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if (p['value'].getClass() == nextflow.util.Duration) {
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new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
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}
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// Cast LinkedHashMap to String
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if (p['value'].getClass() == LinkedHashMap) {
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new_params.replace(p.key, p['value'].toString())
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}
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}
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return new_params
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}
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//
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// This function tries to read a JSON params file
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//
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private static LinkedHashMap paramsLoad(String json_schema) {
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def params_map = new LinkedHashMap()
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try {
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params_map = paramsRead(json_schema)
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} catch (Exception e) {
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println "Could not read parameters settings from JSON. $e"
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params_map = new LinkedHashMap()
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}
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return params_map
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}
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//
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// Method to actually read in JSON file using Groovy.
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// Group (as Key), values are all parameters
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// - Parameter1 as Key, Description as Value
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// - Parameter2 as Key, Description as Value
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// ....
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// Group
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// -
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private static LinkedHashMap paramsRead(String json_schema) throws Exception {
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def json = new File(json_schema).text
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def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
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def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
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/* Tree looks like this in nf-core schema
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* definitions <- this is what the first get('definitions') gets us
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group 1
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title
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description
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properties
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parameter 1
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type
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description
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parameter 2
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type
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description
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group 2
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title
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description
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properties
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parameter 1
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type
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description
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* properties <- parameters can also be ungrouped, outside of definitions
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parameter 1
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type
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description
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*/
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// Grouped params
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def params_map = new LinkedHashMap()
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schema_definitions.each { key, val ->
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def Map group = schema_definitions."$key".properties // Gets the property object of the group
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def title = schema_definitions."$key".title
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def sub_params = new LinkedHashMap()
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group.each { innerkey, value ->
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sub_params.put(innerkey, value)
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}
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params_map.put(title, sub_params)
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|
}
|
|
|
|
// Ungrouped params
|
|
def ungrouped_params = new LinkedHashMap()
|
|
schema_properties.each { innerkey, value ->
|
|
ungrouped_params.put(innerkey, value)
|
|
}
|
|
params_map.put("Other parameters", ungrouped_params)
|
|
|
|
return params_map
|
|
}
|
|
|
|
//
|
|
// Get maximum number of characters across all parameter names
|
|
//
|
|
private static Integer paramsMaxChars(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
|
|
}
|
|
}
|