From 30575ecafde4ea5fd7986bf66ea380b8774d467c Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit Date: Tue, 20 Jan 2026 23:30:07 +0530 Subject: [PATCH 1/4] feat: lifebit related changes for 25.04 version --- .../src/main/groovy/nextflow/cli/CmdRun.groovy | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy index d096e678e6..df3bb95dc7 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -322,6 +322,8 @@ class CmdRun extends CmdBase implements HubOptions { printBanner() Plugins.init() + this.preloadLifebitPlugins() + // -- specify the arguments final scriptFile = getScriptFile(pipeline) @@ -779,4 +781,15 @@ 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 2a24aea245720e9ff0041655f177c334b029dafb Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit Date: Fri, 23 Jan 2026 18:58:04 +0530 Subject: [PATCH 2/4] 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 df3bb95dc7..515f7d022f 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -785,7 +785,7 @@ 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 d2533b0ffbadccae92e182120eb6356c0f97b401 Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit Date: Fri, 23 Jan 2026 19:22:00 +0530 Subject: [PATCH 3/4] 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 515f7d022f..a1d33492bb 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -781,12 +781,12 @@ 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 ) { + 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") } From 050984c635bcfce102ffd384f8e0d8a8f2ae7b02 Mon Sep 17 00:00:00 2001 From: mageshwaran-lifebit Date: Fri, 23 Jan 2026 19:40:26 +0530 Subject: [PATCH 4/4] chore: address copilot 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 a1d33492bb..0b9db73145 100644 --- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy @@ -783,7 +783,7 @@ class CmdRun extends CmdBase implements HubOptions { private void preloadLifebitPlugins() { def envPlugins = sysEnv.get('NXF_LIFEBIT_PRELOAD_PLUGINS') - if( envPlugins ) { + 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}'.")