From 5130c33ea553aa09a27576b6513a5fcf2a2a4cc3 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Thu, 14 Sep 2023 20:50:49 -0500
Subject: [PATCH] Fix inspect command

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 .../groovy/nextflow/cli/CmdInspect.groovy     | 26 +++++++++----------
 .../main/groovy/nextflow/cli/CmdRun.groovy    | 10 ++-----
 .../groovy/nextflow/cli/v2/InspectCmd.groovy  | 14 +++++++++-
 .../main/groovy/nextflow/cli/v2/RunCmd.groovy | 20 +++++++++-----
 4 files changed, 42 insertions(+), 28 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
index 6e113e3917..722a8d6512 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -108,7 +108,18 @@ class CmdInspect {
 
         @Override
         void run() {
-            new CmdInspect(this).run()
+            final opts = new CmdRun.V1()
+            opts.launcher = launcher
+            opts.ansiLog = false
+            opts.preview = true
+            opts.args = args
+            opts.params = params
+            opts.paramsFile = paramsFile
+            opts.profile = profile
+            opts.revision = revision
+            opts.runConfig = runConfig
+
+            new CmdInspect(this).run(opts)
         }
 
     }
@@ -123,21 +134,10 @@ class CmdInspect {
     /* For testing purposes only */
     CmdInspect() {}
 
-    void run() {
+    void run(CmdRun.Options opts) {
         // configure quiet mode
         LoggerHelper.setQuiet(true)
         // setup the target run command
-        final opts = new CmdRun.V1()
-        opts.launcherCli = this.launcherCli
-        opts.launcherOptions = this.launcherOptions
-        opts.args = this.args
-        opts.profile = this.profile
-        opts.revision = this.revision
-        opts.runConfig = this.runConfig
-        opts.params = this.params
-        opts.paramsFile = this.paramsFile
-        opts.preview = true
-        opts.ansiLog = false
         final target = new CmdRun(opts)
         target.previewAction = this.&applyInspect
         // run it
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 0532715932..8f09bca060 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -119,8 +119,6 @@ class CmdRun {
         String getLauncherCli()
         CliOptions getLauncherOptions()
 
-        void setLauncherCli(String launcherCli)
-        void setLauncherOptions(CliOptions launcherOptions)
         void setRunName(String runName)
     }
 
@@ -344,18 +342,14 @@ class CmdRun {
             args.size() > 1 ? args[1..-1] : []
         }
 
-        String launcherCli
-
-        CliOptions launcherOptions
-
         @Override
         String getLauncherCli() {
-            launcherCli ?: launcher.cliString
+            launcher.cliString
         }
 
         @Override
         CliOptions getLauncherOptions() {
-            launcherOptions ?: launcher.options
+            launcher.options
         }
 
         @Override
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/v2/InspectCmd.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/v2/InspectCmd.groovy
index 6b6e2bf49c..fa3e94972f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/v2/InspectCmd.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/v2/InspectCmd.groovy
@@ -110,7 +110,19 @@ class InspectCmd extends AbstractCmd implements CmdInspect.Options {
 
     @Override
     void run() {
-        new CmdInspect(this).run()
+        final opts = new RunCmd()
+        opts.launcher = launcher
+        opts.ansiLog = false
+        opts.preview = true
+        opts.pipeline = pipeline
+        opts.args = args
+        opts.params = params
+        opts.paramsFile = paramsFile
+        opts.profile = profile
+        opts.revision = revision
+        opts.runConfig = runConfig
+
+        new CmdInspect(this).run(opts)
     }
 
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/v2/RunCmd.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/v2/RunCmd.groovy
index 3abcd9852b..49bb3a1057 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/v2/RunCmd.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/v2/RunCmd.groovy
@@ -257,18 +257,26 @@ class RunCmd extends AbstractCmd implements CmdRun.Options, HubOptionsV2 {
         return pipelineParams
     }
 
-    String launcherCli
-
-    CliOptions launcherOptions
-
     @Override
     String getLauncherCli() {
-        launcherCli ?: launcher.cliString
+        launcher.cliString
     }
 
     @Override
     CliOptions getLauncherOptions() {
-        launcherOptions ?: launcher.options
+        launcher.options
+    }
+
+    void setLauncher(Launcher launcher) {
+        this.launcher = launcher
+    }
+
+    void setArgs(List<String> args) {
+        this.pipelineArgs = args
+    }
+
+    void setParams(Map<String,String> params) {
+        this.pipelineParams = params
     }
 
     @Override