Error handling already existing write-protected plugins-folder

[asp8200]

Bug report

We have a write-protected shared plugins-folder containing all plugins needed for running sarek v3.6.1, but NF tries to create the already existing plugins-folder:

$ sarek -profile test
NEXTFLOW ~ version 25.10.0
ERROR ~ Unable to create plugins dir: /ngc/tools/bin/nextflow/plugins

The plugins-folder /ngc/tools/bin/nextflow/plugins already exists, and it contains the needed plugins.

I'm running with
NXF_PLUGINS_DIR=/ngc/tools/bin/nextflow/plugins
NXF_OFFLINE=true
NXF_PLUGINS_DEFAULT=false

Expected behavior and actual behavior

NF shouldn't try to create the plugins-folder if it already exists. According to @jagedn, it might just be a matter of checking here whether the plugins-folder already exists.

Steps to reproduce the problem

I guess one can reproduce it by using a write-protected plugins-folder.

Program output

From .nextflow.log :

java.nio.file.FileSystemException: /ngc/tools/bin/nextflow/plugins: Read-only file system
at java.base/sun.nio.fs.UnixException.translateTo10Exception(UnixException.java: 100)
at java.base/sun.nio.fs.UnixException.rethrowAsI0Exception(UnixException.java: 106)
java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java: 111)
java.base/sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:418)
at java.base/java.nio.file.Files.createDirectory(Files.java:647)
java.base/java.nio.file.Files.createAndCheckIsDirectory(Files.java:734)
java.base/java.nio.file.Files.createDirectories (Files.java:720)
org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
nextflow.extension.FilesEx.mkdirs(FilesEx.groovy:493)
nextflow.plugin.PluginsFacade. init(PluginsFacade.groovy:258)
nextflow.plugin.plugins. init(Plugins.groovy:39)
nextflow.plugin.Plugins.init(Plugins.groovy)
nextflow.cli.CmdRun.run(CmdRun.groovy:362)
at nextflow.cli.Launcher.run(Launcher.groovy:515 )
at nextflow.cli.Launcher.main(Launcher.groovy:675)
Nov-13 14:20:53.856 [main] ERROR nextflow.cli.Launcher - Unable to create plugins dir: /ngc/tools/bin/nextflow/plugins

Environment

• Nextflow version: 25.10.0 (but same behaviour on other versions of NF)
• Java version: 25+36 (but same behaviour on other versions of Java)
• Operating system: Rocky Linux v9.6

Additional context

The plugins-folder is on a shared NFS-drive. I'm running on a HPC with no internet-connection.

I had a conversion with @jagedn on slack about this issue.

[asp8200]

I believe I hacked my way around the issue by rsyncing the plugins from the shared write-protected plugins-folder to the users home-folder. Here is my wrapper script

$ cat sarek
#/bin/bash
rsync -a $NXF_PLUGINS_DIR $HOME/.nextflow
NXF_PLUGINS_DIR=$HOME/.nextflow/plugins nextflow run /ngc/tools/ngctools/sarek/3.6.1/assets/nf-core/sarek/main.nf  $@

[JPWerling]

I am encountering the same issue. I need to ensure no users are able to modify the pipeline once installed, and being forced to allow write access to the plugins directory risks accidental tampering.

[bentsherman]

I went ahead and submitted a PR since the change seems reasonable, but I haven't actually been able to reproduce the error locally yet:

export NXF_PLUGINS_DIR="$PWD/plugins"

if [ -e "$NXF_PLUGINS_DIR" ] ; then
    sudo chattr -i "$NXF_PLUGINS_DIR"
    rm -rf "$NXF_PLUGINS_DIR"
fi

mkdir -p "$NXF_PLUGINS_DIR"
nextflow plugin install nf-hello@0.5.0
sudo chattr +i "$NXF_PLUGINS_DIR"

export NXF_OFFLINE=true
export NXF_PLUGINS_DEFAULT=false

nextflow run hello

// nextflow.config
plugins {
    id 'nf-hello@0.5.0'
}

Maybe my Bash-fu is lacking something, but I guess the error could also depend on the OS, particularly its implementation of mkdirs

[asp8200]

Thanks for looking into this, Ben.

The shared drive on our HPC doesn't support a command like chattr +i; I think we ran chmod 744 on the shared plugins-folder, but I can't check right now.

I can't reproduce the issue on my own linux-box, so the issue does indeed seem to be OS dependent.