From 355ee09d1534b6eed4edc23d75bf21c12ed885ca Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit Date: Tue, 20 Jan 2026 23:28:02 +0530 Subject: [PATCH 1/3] feat: lifebit related changes for 25.10 version --- .../src/main/groovy/nextflow/cli/CmdRun.groovy | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy index e43801459a..a5dc919b47 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -325,6 +325,8 @@ class CmdRun extends CmdBase implements HubOptions { Plugins.init() + this.preloadLifebitPlugins() + // -- resolve main script final scriptFile = getScriptFile(pipeline) @@ -829,4 +831,14 @@ 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") + } + } } From c4bc11311f45e572b756bd90879fb407e56b4e24 Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit <121040241+mageshwaran-lifebit@users.noreply.github.com> Date: Fri, 23 Jan 2026 19:01:11 +0530 Subject: [PATCH 2/3] chore: address cursor comment --- modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy index a5dc919b47..12792ca6a9 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -835,7 +835,7 @@ class CmdRun extends CmdBase implements HubOptions { def plugins = sysEnv.get('NXF_LIFEBIT_PRELOAD_PLUGINS') if( plugins ) { log.debug("Pre-loading Lifebit's plugins '${plugins}'...") - Plugins.load([plugins: plugins.tokenize(',')]) + Plugins.load([plugins: plugins.tokenize(',').collect { it.trim() }]) log.debug("Preloaded Lifebit's plugins '${plugins}'.") } else { log.debug("No Lifebit's plugins to pre-load") From 25fb9637376001972d0a194216e9eab310e69e39 Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit <121040241+mageshwaran-lifebit@users.noreply.github.com> Date: Fri, 23 Jan 2026 19:56:12 +0530 Subject: [PATCH 3/3] chore: address Copilot comment --- .../src/main/groovy/nextflow/cli/CmdRun.groovy | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy index 12792ca6a9..1125c7d5d2 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -831,12 +831,12 @@ 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 '${plugins}'...") - Plugins.load([plugins: plugins.tokenize(',').collect { it.trim() }]) - log.debug("Preloaded Lifebit's plugins '${plugins}'.") + private void preloadLifebitPlugins() { + def envPlugins = sysEnv.get('NXF_LIFEBIT_PRELOAD_PLUGINS') + if( envPlugins && envPlugins.trim().length() > 0 ) { + log.debug("Pre-loading Lifebit's plugins '${envPlugins}'...") + Plugins.load([plugins: envPlugins.tokenize(',').collect { it.trim() }.findAll { it }.unique()]) + log.debug("Preloaded Lifebit's plugins '${envPlugins}'.") } else { log.debug("No Lifebit's plugins to pre-load") }