diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
index b057f409c3..b4701aacd3 100644
--- a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy
@@ -508,9 +508,7 @@ class ConfigBuilder {
             if( !(config.trace instanceof Map) )
                 config.trace = [:]
             config.trace.enabled = true
-            if( !config.trace.file )
-                config.trace.file = cmdRun.withTrace
-
+            config.trace.file = cmdRun.withTrace
         }
 
         // -- sets report report options
@@ -518,8 +516,7 @@ class ConfigBuilder {
             if( !(config.report instanceof Map) )
                 config.report = [:]
             config.report.enabled = true
-            if( !config.report.file )
-                config.report.file = cmdRun.withReport
+            config.report.file = cmdRun.withReport
         }
 
         // -- sets timeline report options
@@ -527,8 +524,7 @@ class ConfigBuilder {
             if( !(config.timeline instanceof Map) )
                 config.timeline = [:]
             config.timeline.enabled = true
-            if( !config.timeline.file )
-                config.timeline.file = cmdRun.withTimeline
+            config.timeline.file = cmdRun.withTimeline
         }
 
         // -- sets DAG report options
@@ -536,8 +532,7 @@ class ConfigBuilder {
             if( !(config.dag instanceof Map) )
                 config.dag = [:]
             config.dag.enabled = true
-            if( !config.dag.file )
-                config.dag.file = cmdRun.withDag
+            config.dag.file = cmdRun.withDag
         }
 
         if( cmdRun.withNotification ) {
@@ -557,8 +552,7 @@ class ConfigBuilder {
             if( !(config.weblog instanceof Map) )
                 config.weblog = [:]
             config.weblog.enabled = true
-            if ( !config.weblog.url )
-                config.weblog.url = cmdRun.withWebLog
+            config.weblog.url = cmdRun.withWebLog
         }
 
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
index 7a1ef780a5..4b36919c53 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy
@@ -610,49 +610,191 @@ class ConfigBuilderTest extends Specification {
 
         given:
         def env = [:]
-        def config = new ConfigObject()
         def builder = [:] as ConfigBuilder
 
         when:
-        config.trace.enabled = true
+        def config = new ConfigObject()
         builder.configRunOptions(config, env, new CmdRun())
 
         then:
         config.trace instanceof Map
-        config.trace.enabled
+        !config.trace.enabled
         !config.trace.file
 
         when:
+        config = new ConfigObject()
         builder.configRunOptions(config, env, new CmdRun(withTrace: 'some-file'))
         then:
         config.trace instanceof Map
         config.trace.enabled
         config.trace.file == 'some-file'
 
+        when:
+        config = new ConfigObject()
+        config.trace.file = 'foo.txt'
+        builder.configRunOptions(config, env, new CmdRun(withTrace: 'bar.txt'))
+        then: // command line should override the config file
+        config.trace instanceof Map
+        config.trace.enabled
+        config.trace.file == 'bar.txt'
+
     }
 
-    def 'should set session timeline options' () {
+    def 'should set session report options' () {
 
         given:
         def env = [:]
+        def builder = [:] as ConfigBuilder
+
+        when:
         def config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        !config.report
+
+        when:
+        config = new ConfigObject()
+        config.report.file = 'foo.html'
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        config.report instanceof Map
+        !config.report.enabled
+        config.report.file == 'foo.html'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(withReport: 'my-report.html'))
+        then:
+        config.report instanceof Map
+        config.report.enabled
+        config.report.file == 'my-report.html'
+
+        when:
+        config = new ConfigObject()
+        config.report.file = 'this-report.html'
+        builder.configRunOptions(config, env, new CmdRun(withReport: 'my-report.html'))
+        then:
+        config.report instanceof Map
+        config.report.enabled
+        config.report.file == 'my-report.html'
+
+    }
+
+
+    def 'should set session dag options' () {
+
+        given:
+        def env = [:]
         def builder = [:] as ConfigBuilder
 
         when:
+        def config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        !config.dag
+
+        when:
+        config = new ConfigObject()
+        config.dag.file = 'foo-dag.html'
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        config.dag instanceof Map
+        !config.dag.enabled
+        config.dag.file == 'foo-dag.html'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(withDag: 'my-dag.html'))
+        then:
+        config.dag instanceof Map
+        config.dag.enabled
+        config.dag.file == 'my-dag.html'
+
+        when:
+        config = new ConfigObject()
+        config.dag.file = 'this-dag.html'
+        builder.configRunOptions(config, env, new CmdRun(withDag: 'my-dag.html'))
+        then:
+        config.dag instanceof Map
+        config.dag.enabled
+        config.dag.file == 'my-dag.html'
+
+    }
+
+    def 'should set session weblog options' () {
+
+        given:
+        def env = [:]
+        def builder = [:] as ConfigBuilder
+
+        when:
+        def config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        !config.weblog
+
+        when:
+        config = new ConfigObject()
+        config.weblog.url = 'http://bar.com'
+        builder.configRunOptions(config, env, new CmdRun())
+        then:
+        config.weblog instanceof Map
+        !config.weblog.enabled
+        config.weblog.url == 'http://bar.com'
+
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(withWebLog: 'http://foo.com'))
+        then:
+        config.weblog instanceof Map
+        config.weblog.enabled
+        config.weblog.url == 'http://foo.com'
+
+        when:
+        config = new ConfigObject()
+        config.weblog.enabled = true
+        config.weblog.url = 'http://bar.com'
+        builder.configRunOptions(config, env, new CmdRun(withWebLog: 'http://foo.com'))
+        then:
+        config.weblog instanceof Map
+        config.weblog.enabled
+        config.weblog.url == 'http://foo.com'
+
+    }
+
+    def 'should set session timeline options' () {
+
+        given:
+        def env = [:]
+        def builder = [:] as ConfigBuilder
+
+        when:
+        def config = new ConfigObject()
         builder.configRunOptions(config, env, new CmdRun())
         then:
         !config.timeline
 
         when:
-        config.timeline.enabled = true
+        config = new ConfigObject()
+        config.timeline.file = 'my-file.html'
         builder.configRunOptions(config, env, new CmdRun())
+        then:
+        config.timeline instanceof Map
+        !config.timeline.enabled
+        config.timeline.file == 'my-file.html'
 
+        when:
+        config = new ConfigObject()
+        builder.configRunOptions(config, env, new CmdRun(withTimeline: 'my-timeline.html'))
         then:
         config.timeline instanceof Map
         config.timeline.enabled
-        !config.timeline.file
+        config.timeline.file == 'my-timeline.html'
 
         when:
+        config = new ConfigObject()
+        config.timeline.enabled = true
+        config.timeline.file = 'this-timeline.html'
         builder.configRunOptions(config, env, new CmdRun(withTimeline: 'my-timeline.html'))
         then:
         config.timeline instanceof Map
@@ -661,15 +803,14 @@ class ConfigBuilderTest extends Specification {
 
     }
 
-
     def 'SHOULD SET `RESUME` OPTION'() {
 
         given:
         def env = [:]
-        def config = new ConfigObject()
         def builder = [:] as ConfigBuilder
 
         when:
+        def config = new ConfigObject()
         builder.configRunOptions(config, env, new CmdRun())
         then:
         !config.isSet('resume')
@@ -688,6 +829,12 @@ class ConfigBuilderTest extends Specification {
         then:
         config.resume == 'xxx-yyy'
 
+        when:
+        config = new ConfigObject()
+        config.resume ='this-that'
+        builder.configRunOptions(config, env, new CmdRun(resume: 'xxx-yyy'))
+        then:
+        config.resume == 'xxx-yyy'
     }
 
     def 'should set `workDir`' () {