diff --git a/docs/reference/cli.md b/docs/reference/cli.md index 5a7f15c23c..23874f2ec5 100644 --- a/docs/reference/cli.md +++ b/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-.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-.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-.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). diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy index d096e678e6..356b0f397b 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/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) diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy index 6afda06942..8ba72b764d 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/Launcher.groovy +++ b/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 << '-' } diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy index 2527d1bac1..bc55b065dc 100644 --- a/modules/nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy +++ b/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'] diff --git a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy b/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy index 18c331a073..a0c0dbd66c 100644 --- a/modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy +++ b/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) && !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' } ) {