bump to v1.0.3

Author: rpetit3

CHANGELOG.md

@@ -1,5 +1,9 @@
 # bactopia/nf-bactopia: Changelog
 
+## v1.0.3
+
+- Expose the config options
+
 ## v1.0.2
 
 - bump to latest nextflow gradle plugin version

build.gradle

@@ -9,7 +9,7 @@ dependencies {
     implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
 }
 
-version = '1.0.2'
+version = '1.0.3'
 
 nextflowPlugin {
     nextflowVersion = '25.10.0'
@@ -18,6 +18,7 @@ nextflowPlugin {
     description = 'A plugin for working with Bactopia'
     className = 'bactopia.plugin.BactopiaPlugin'
     extensionPoints = [
+        'bactopia.plugin.BactopiaConfig',
         'bactopia.plugin.BactopiaExtension',
         'bactopia.plugin.BactopiaFactory'
     ]

src/main/groovy/bactopia/plugin/BactopiaConfig.groovy

@@ -2,9 +2,9 @@ package bactopia.plugin
 
 import groovy.util.logging.Slf4j
 
-import nextflow.config.schema.ConfigOption
-import nextflow.config.schema.ConfigScope
-import nextflow.config.schema.ScopeName
+import nextflow.config.spec.ConfigOption
+import nextflow.config.spec.ConfigScope
+import nextflow.config.spec.ScopeName
 import nextflow.script.dsl.Description
 
 /**
@@ -20,13 +20,23 @@ import nextflow.script.dsl.Description
 @Description('''
     The `bactopia` scope allows you to configure the `nf-bactopia` plugin.
 ''')
-class BactopiaConfig  implements ConfigScope  {
+class BactopiaConfig implements ConfigScope  {
 
+    @ConfigOption
+    @Description('Enable monochrome logs.')
     final public Boolean monochromeLogs = false
 
-    final public CharSequence  parametersSchema = "nextflow_schema.json"
+    @ConfigOption
+    @Description('Path to the parameters schema file.')
+    final public CharSequence parametersSchema = "nextflow_schema.json"
+
+    @ConfigOption
+    @Description('Ignore specific parameters.')
     final public Set<CharSequence> ignoreParams = [] // Defaults will be set on the Bactopia side
 
+    // Keep the no-arg constructor in order to be able to use the `@ConfigOption` annotation
+    BactopiaConfig(){}
+
     BactopiaConfig(Map map, Map params){
         def config = map ?: Collections.emptyMap()
 
@@ -40,7 +50,7 @@ class BactopiaConfig  implements ConfigScope  {
             }
         }
 
-        // parameterSchema
+        // parametersSchema
         if(config.containsKey("parametersSchema")) {
             if(config.parametersSchema instanceof CharSequence) {
                 parametersSchema = config.parametersSchema

src/main/groovy/bactopia/plugin/BactopiaExtension.groovy

@@ -107,110 +107,6 @@ class BactopiaExtension extends PluginExtensionPoint {
     }
 
 
-    //
-    // Groovy Map of the help message
-    //
-    @Function
-    public String paramsHelp() {
-        def Map params = session.params
-        def String help = ""
-        def HelpMessageCreator helpCreator = new HelpMessageCreator(config, session, params["help_all"])
-        help += helpCreator.getBeforeText(session, (String) params["workflow"]["name"], (String) params["workflow"]["description"])
-        if (params["help_all"]) {
-            log.debug("Printing out the full help message")
-            help += helpCreator.getFullMessage()
-        } else if (params["help"]) {
-            log.debug("Printing out the short help message")
-            def paramValue = null
-            help += helpCreator.getShortMessage(paramValue instanceof String ? paramValue : "")
-        }
-        help += helpCreator.getAfterText()
-        return help
-    }
-
-    //
-    // Groovy Map summarising parameters/workflow options used by the pipeline
-    //
-    @Function
-    public Map paramsSummaryMap(
-        Map options = null,
-        WorkflowMetadata workflow
-        ) {
-        def SummaryCreator creator = new SummaryCreator(config)
-        return creator.getSummaryMap(
-            options,
-            workflow,
-            session.baseDir.toString(),
-            session.params
-        )
-    }
-
-    /*
-     * Beautify parameters for summary and return as string
-     */
-    @Function
-    public String paramsSummaryLog(
-        Map options = null,
-        WorkflowMetadata workflow
-    ) {
-        def Map params = session.params
-        def String schemaFilename = options?.containsKey('parameters_schema') ? options.parameters_schema as String : config.parametersSchema
-
-        def colors = getLogColors(config.monochromeLogs)
-        String output = ''
-        output += getLogo(workflow, config.monochromeLogs, params.workflow.name, params.workflow.description)
-
-        def Map paramsMap = paramsSummaryMap(workflow, parameters_schema: schemaFilename)
-        paramsMap.each { key, value ->
-            paramsMap[key] = flattenNestedParamsMap(value as Map)
-        }
-        def maxChars  = getLongestKeyLength(paramsMap)
-        for (group in paramsMap.keySet()) {
-            def Map group_params = paramsMap.get(group) as Map // This gets the parameters of that particular group
-            if (group_params) {
-                output += "$colors.bold$group$colors.reset\n"
-                for (String param in group_params.keySet()) {
-                    output += "  " + colors.blue + param.padRight(maxChars) + ": " + colors.green +  group_params.get(param) + colors.reset + '\n'
-                }
-                output += '\n'
-            }
-        }
-        output += "!! Only displaying parameters that differ from the defaults !!\n"
-        output += dashedLine(config.monochromeLogs) + "\n"
-        return output
-    }
-
-    /*
-     * Beautify parameters for summary and return as string
-     */
-    @Function
-    public String workflowSummary() {
-        def Map params = session.params
-        def WorkflowMetadata metadata = session.getWorkflowMetadata()
-        return getWorkflowSummary( 
-            metadata,
-            params,
-            session.config.manifest.version,
-            config.monochromeLogs,
-        )
-    }
-
-    private Map flattenNestedParamsMap(Map paramsMap) {
-        def Map returnMap = [:]
-        paramsMap.each { param, value ->
-            def String key = param as String
-            if (value instanceof Map) {
-                def Map flatMap = flattenNestedParamsMap(value as Map)
-                flatMap.each { flatParam, flatValue ->
-                    returnMap.put(key + "." + flatParam, flatValue)
-                }
-            } else {
-                returnMap.put(key, value)
-            }
-        }
-        return returnMap
-    }
-
     /*
     * Function to loop over all parameters defined in schema and check
     * whether the given parameters adhere to the specifications

src/main/groovy/bactopia/plugin/BactopiaFactory.groovy

@@ -17,6 +17,7 @@
 package bactopia.plugin
 
 import groovy.transform.CompileStatic
+
 import nextflow.Session
 import nextflow.trace.TraceObserverV2
 import nextflow.trace.TraceObserverFactoryV2
@@ -32,8 +33,13 @@ class BactopiaFactory implements TraceObserverFactoryV2 {
 
     @Override
     Collection<TraceObserverV2> create(Session session) {
-        final result = new ArrayList()
-        result.add( new BactopiaObserver() )
+        final result = new ArrayList<TraceObserverV2>()
+        result.add( 
+            new BactopiaObserver(
+                session,
+                new BactopiaConfig(session?.config?.navigate('bactopia') as Map, session.params)
+            ) 
+        )
         return result
     }
 }

src/main/groovy/bactopia/plugin/BactopiaObserver.groovy

@@ -20,10 +20,17 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import java.nio.file.Path
 import java.nio.file.Paths
+
 import nextflow.Session
+import nextflow.script.WorkflowMetadata
 import nextflow.trace.TraceObserverV2
 
+import bactopia.plugin.BactopiaConfig
 import static bactopia.plugin.BactopiaMotD.getMotD
+import static bactopia.plugin.BactopiaTemplate.getWorkflowSummary
+import static bactopia.plugin.BactopiaUtils.paramsHelp
+import static bactopia.plugin.BactopiaUtils.paramsSummaryLog
+import static bactopia.plugin.BactopiaUtils.validateParameters
 
 /**
  * Bactopia workflow observer
@@ -34,11 +41,47 @@ import static bactopia.plugin.BactopiaMotD.getMotD
 @Slf4j
 class BactopiaObserver implements TraceObserverV2 {
 
+    private Session session
+    BactopiaConfig config
+
+    BactopiaObserver(
+        Session session,
+        BactopiaConfig config
+    ) {
+        this.session = session
+        this.config = config
+    }
+
     @Override
-    void onFlowCreate(Session session) {}
+    void onFlowCreate(Session session) {
+        def Map params = this.session.params
+        def WorkflowMetadata metadata = this.session.getWorkflowMetadata()
+        if (params["help"] || params["help_all"]) {
+            println paramsHelp(session, config)
+            System.exit(0)
+        } else {
+            // print params summary
+            println paramsSummaryLog(
+                metadata,
+                this.session,
+                this.config,
+                null
+            )
+        }
+    }
 
     @Override
-    void onFlowComplete() {}
+    void onFlowComplete() {
+        def Map params = this.session.params
+        def WorkflowMetadata metadata = this.session.getWorkflowMetadata()
+        println getWorkflowSummary( 
+            metadata,
+            params,
+            this.session.config.manifest.version,
+            this.config.monochromeLogs,
+        )
+
+    }
 
     void onWorkflowPublish(String name, Object value) {}
     void onFilePublish(Path destination, Path source, Map annotations) {}