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Field 'id' cannot be empty #38

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Bo-UT opened this issue Nov 16, 2024 · 1 comment
Open

Field 'id' cannot be empty #38

Bo-UT opened this issue Nov 16, 2024 · 1 comment

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@Bo-UT
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Bo-UT commented Nov 16, 2024

Hi
I am new to nextflow. I ran sarek-3.4.4 for mutect2 on the server. Our server is offline. I downloaded [email protected] from https://github.com/nextflow-io/nf-prov/releases/download/1.2.2/nf-prov-1.2.2.zip, and moved it to ~/.nextflow/plugins. I constantly got the error

Nov-16 12:32:26.791 [main] ERROR nextflow.cli.Launcher - @unknown
org.pf4j.InvalidPluginDescriptorException: Field 'id' cannot be empty

The log file is

Error log Nov-16 12:32:26.424 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[[email protected], [email protected]] Nov-16 12:32:26.425 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Nov-16 12:32:26.425 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[[email protected], [email protected]] Nov-16 12:32:26.429 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 Nov-16 12:32:26.454 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved Nov-16 12:32:26.455 [main] INFO org.pf4j.AbstractPluginManager - Start plugin '[email protected]' Nov-16 12:32:26.775 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected] Nov-16 12:32:26.775 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-prov version: 1.2.2 Nov-16 12:32:26.791 [main] ERROR nextflow.cli.Launcher - @unknown org.pf4j.InvalidPluginDescriptorException: Field 'id' cannot be empty at org.pf4j.AbstractPluginManager.validatePluginDescriptor(AbstractPluginManager.java:989) at org.pf4j.AbstractPluginManager.loadPluginFromPath(AbstractPluginManager.java:895) at org.pf4j.DefaultPluginManager.loadPluginFromPath(DefaultPluginManager.java:139) at nextflow.plugin.CustomPluginManager.loadPluginFromPath(CustomPluginManager.groovy:46) at nextflow.plugin.LocalPluginManager.loadPluginFromPath(LocalPluginManager.groovy:98) at nextflow.plugin.PluginUpdater.load0(PluginUpdater.groovy:342) at nextflow.plugin.PluginUpdater.installPlugin(PluginUpdater.groovy:198) at nextflow.plugin.PluginUpdater.prepareAndStart(PluginUpdater.groovy:145) at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:335) at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:340) at nextflow.plugin.PluginsFacade.load(PluginsFacade.groovy:239) at nextflow.plugin.Plugins.load(Plugins.groovy:52) at nextflow.cli.CmdRun.run(CmdRun.groovy:342) at nextflow.cli.Launcher.run(Launcher.groovy:503) at nextflow.cli.Launcher.main(Launcher.groovy:658)

The code I used to run nextflow

nextflow run $WORKFLOW \
--genome null --igenomes_ignore --fasta $REF_FASTA \
-profile singularity \
--save_output_as_bam \
-c $CONFIG \
--tools mutect2 \
--input $SAMPLE_SHEET \
--outdir $GATK_RESULT

Thanks for your help!

@Bo-UT
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Bo-UT commented Nov 16, 2024

I add the plugins setting in the .config file, but that doesn't help. The nextflow version I am using is 24.10.0.

plugins {
  id '[email protected]'
}

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