feat: lifebit related changes for 25.04 version#32
feat: lifebit related changes for 25.04 version#32mageshwaran-lifebit merged 4 commits into25.04.8from
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We need to add branch protection rules for this branch @mageshwaran-lifebit . Are you able to do it?
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Pull request overview
Adds support for pre-loading Lifebit plugins in the Nextflow run command, based on an environment variable, so specified plugins are loaded before pipeline execution.
Changes:
- Invoke a new preloading hook during
CmdRun.run()initialization (afterPlugins.init()). - Add
preloadLifebitPlugins()to readNXF_LIFEBIT_PRELOAD_PLUGINSand load the listed plugins via the plugin subsystem.
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Pull request overview
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| 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}'.") | ||
| } else { | ||
| log.debug("No Lifebit's plugins to pre-load") | ||
| } |
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There are existing unit tests for CmdRun (e.g. modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy). The new env-driven plugin preloading behavior isn’t covered; adding a test that verifies parsing/normalization of NXF_LIFEBIT_PRELOAD_PLUGINS and that the plugin loader is invoked with the expected ids (including edge-cases like whitespace/trailing commas) would help prevent regressions.
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This pull request adds support for pre-loading Lifebit plugins in the Nextflow CLI. The main change is the introduction of a method that checks for a specific environment variable and loads the specified plugins before pipeline execution.
Lifebit plugin pre-loading:
preloadLifebitPluginsmethod toCmdRun, which checks theNXF_LIFEBIT_PRELOAD_PLUGINSenvironment variable and loads the listed plugins if present.preloadLifebitPluginsmethod during command initialization, ensuring Lifebit plugins are loaded before pipeline execution.