feat: Lifebit's related changes on 22.10.8 version (#26)

.gitignore

@@ -36,4 +36,5 @@ gradle.properties
 .launch.classpath
 plugins-prod
 sandbox
-wave-demo
+wave-demo
+.DS_Store

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -839,7 +839,7 @@ class Session implements ISession {
         // an exception is thrown is the version does not match
         boolean important = false
         if( version.startsWith('!') ) {
-            important = true
+//            important = true // commenting to avoid pipeline failure due to lower version. https://github.com/nf-core/raredisease/blob/master/nextflow.config#L295C5-L295C35
             version = version.substring(1).trim()
         }
 

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -296,6 +296,8 @@ class CmdRun extends CmdBase implements HubOptions {
         log.info "N E X T F L O W  ~  version ${Const.APP_VER}"
         Plugins.init()
 
+        this.preloadLifebitPlugins()
+
         // -- specify the arguments
         final scriptFile = getScriptFile(pipeline)
 
@@ -678,4 +680,15 @@ class CmdRun extends CmdBase implements HubOptions {
         }
     }
 
+    void preloadLifebitPlugins() {
+        def plugins = sysEnv.get('NXF_LIFEBIT_PRELOAD_PLUGINS')
+        if( plugins ) {
+            log.debug("Pre-loading Lifebit's plugins '${plugins}'...")
+            Plugins.load([plugins: plugins.tokenize(',')])
+            log.debug("Preloaded Lifebit's plugins '${plugins}'.")
+        } else {
+            log.debug("No Lifebit's plugins to pre-load")
+        }
+    }
+
 }