♻️ refactor(cli): add -with-seqera and SEQERA_ACCESS_TOKEN as aliases for nextflow run

docs/reference/cli.md

@@ -631,9 +631,9 @@ The `kuberun` command supports the following options from [`run`](#run):
 - `-with-dag`
 - `-N, -with-notification`
 - `-with-report`
+- `-with-seqera`
 - `-with-spack`
 - `-with-timeline`
-- `-with-tower`
 - `-with-trace`
 - `-with-wave`
 - `-with-weblog`
@@ -1194,6 +1194,9 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-report` (`report-<timestamp>.html`)
 : Create workflow execution HTML report.
 
+`-with-seqera`, `-with-tower` (`https://api.cloud.seqera.io`)
+: Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
+
 `-with-singularity`
 : Enable process execution in a Singularity container.
 
@@ -1203,9 +1206,6 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 `-with-timeline` (`timeline-<timestamp>.html`)
 : Create workflow execution timeline.
 
-`-with-tower` (`https://api.cloud.seqera.io`)
-: Monitor workflow execution with [Seqera Platform](https://seqera.io/) (formerly Tower Cloud).
-
 `-with-trace` (`trace-<timestamp>.txt`)
 : Create workflow execution trace file.
 
@@ -1271,7 +1271,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline
 - Execute a pipeline with integrated monitoring in [Seqera Platform](https://seqera.io).
 
   ```console
-  $ nextflow run nextflow-io/hello -with-tower
+  $ nextflow run nextflow-io/hello -with-seqera
   ```
 
 - Execute a pipeline with a custom parameters file (YAML or JSON).

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

@@ -167,7 +167,7 @@ class CmdRun extends CmdBase implements HubOptions {
         launcher.options.ansiLog = value
     }
 
-    @Parameter(names = ['-with-tower'], description = 'Monitor workflow execution with Seqera Platform (formerly Tower Cloud)')
+    @Parameter(names = ['-with-tower', '-with-seqera'], description = 'Monitor workflow execution with Seqera Platform (formerly Tower Cloud)')
     String withTower
 
     @Parameter(names = ['-with-wave'], hidden = true)

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

@@ -293,7 +293,7 @@ class Launcher {
                 normalized << '-'
             }
 
-            else if( current == '-with-tower' && (i==args.size() || args[i].startsWith('-'))) {
+            else if( (current == '-with-tower' || current == '-with-seqera') && (i==args.size() || args[i].startsWith('-'))) {
                 normalized << '-'
             }
 

modules/nextflow/src/main/groovy/nextflow/platform/PlatformHelper.groovy

@@ -30,16 +30,17 @@ class PlatformHelper {
     /**
      * Return the configured Platform access token: if `TOWER_WORKFLOW_ID` is provided in the environment, it means
      * we are running in a Platform-made run and we should ONLY retrieve the token from the environment. Otherwise,
-     * check the configuration or fallback to the environment. If no token is found, return null.
+     * check the configuration or fallback to the environment. The access token can be provided via either
+     * SEQERA_ACCESS_TOKEN (preferred) or TOWER_ACCESS_TOKEN environment variables. If no token is found, return null.
      *
      * @param opts the configuration options for Platform (e.g. `session.config.navigate('tower')`)
      * @param env the applicable environment variables
      * @return the Platform access token
      */
     static String getAccessToken(Map opts, Map<String,String> env) {
         final token = env.get('TOWER_WORKFLOW_ID')
-            ? env.get('TOWER_ACCESS_TOKEN')
-            : opts.containsKey('accessToken') ? opts.accessToken as String : env.get('TOWER_ACCESS_TOKEN')
+            ? (env.get('SEQERA_ACCESS_TOKEN') ?: env.get('TOWER_ACCESS_TOKEN'))
+            : opts.containsKey('accessToken') ? opts.accessToken as String : (env.get('SEQERA_ACCESS_TOKEN') ?: env.get('TOWER_ACCESS_TOKEN'))
         return token
     }
 

modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy

@@ -195,6 +195,10 @@ class LauncherTest extends Specification {
         launcher.normalizeArgs('run','-with-tower', '-x') == ['run', '-with-tower', '-', '-x']
         launcher.normalizeArgs('run','-with-tower', 'foo.com') == ['run', '-with-tower','foo.com']
 
+        launcher.normalizeArgs('run','-with-seqera') == ['run', '-with-seqera', '-']
+        launcher.normalizeArgs('run','-with-seqera', '-x') == ['run', '-with-seqera', '-', '-x']
+        launcher.normalizeArgs('run','-with-seqera', 'foo.com') == ['run', '-with-seqera','foo.com']
+
         launcher.normalizeArgs('run','-with-wave') == ['run', '-with-wave', '-']
         launcher.normalizeArgs('run','-with-wave', '-x') == ['run', '-with-wave', '-', '-x']
         launcher.normalizeArgs('run','-with-wave', 'foo.com') == ['run', '-with-wave','foo.com']

modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy

@@ -430,7 +430,7 @@ class PluginsFacade implements PluginStateListener {
         }
 
         // add tower plugin when config contains tower options
-        if( (Bolts.navigate(config,'tower.enabled') || Bolts.navigate(config,'fusion.enabled') || env.TOWER_ACCESS_TOKEN ) && !specs.find {it.id == 'nf-tower' } ) {
+        if( (Bolts.navigate(config,'tower.enabled') || Bolts.navigate(config,'fusion.enabled') || env.TOWER_ACCESS_TOKEN || env.SEQERA_ACCESS_TOKEN) && !specs.find {it.id == 'nf-tower' } ) {
             specs << defaultPlugins.getPlugin('nf-tower')
         }
         if( (Bolts.navigate(config,'wave.enabled') || Bolts.navigate(config,'fusion.enabled')) && !specs.find {it.id == 'nf-wave' } ) {

plugins/nf-tower/src/main/io/seqera/tower/plugin/TowerClient.groovy

@@ -378,15 +378,19 @@ class TowerClient implements TraceObserver {
         log.info(LoggerHelper.STICKY, msg)
     }
 
+    /**
+     * Get the access token for Seqera Platform authentication.
+     * When 'TOWER_WORKFLOW_ID' is provided in the env, it's a tower made launch
+     * therefore the access token should only be taken from the env.
+     * Otherwise check into the config file and fallback in the env.
+     * The access token can be provided via either SEQERA_ACCESS_TOKEN (preferred) or TOWER_ACCESS_TOKEN environment variables.
+     */
     String getAccessToken() {
-        // when 'TOWER_WORKFLOW_ID' is provided in the env, it's a tower made launch
-        // therefore the access token should only be taken from the env
-        // otherwise check into the config file and fallback in the env
         def token = env.get('TOWER_WORKFLOW_ID')
-                ? env.get('TOWER_ACCESS_TOKEN')
-                : session.config.navigate('tower.accessToken', env.get('TOWER_ACCESS_TOKEN'))
+                ? (env.get('SEQERA_ACCESS_TOKEN') ?: env.get('TOWER_ACCESS_TOKEN'))
+                : session.config.navigate('tower.accessToken', env.get('SEQERA_ACCESS_TOKEN') ?: env.get('TOWER_ACCESS_TOKEN'))
         if( !token )
-            throw new AbortOperationException("Missing Seqera Platform access token -- Make sure there's a variable TOWER_ACCESS_TOKEN in your environment")
+            throw new AbortOperationException("Missing Seqera Platform access token -- Make sure there's a variable SEQERA_ACCESS_TOKEN or TOWER_ACCESS_TOKEN in your environment")
         return token
     }