Grape not supported anymore on Nextflow version v24.0.7.0-edge

[VasLem]

Bug report

The following piece of code works in v24.06,0-edge but not in the latest version:

@Grab(group='org.apache.commons', module='commons-text', version='1.12.0')
import org.apache.commons.text.similarity.LevenshteinDistance

Program output

ERROR ~ Class definition not found: org/apache/ivy/util/MessageLogger

...
Aug-17 20:03:02.815 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.NoClassDefFoundError: org/apache/ivy/util/MessageLogger
	at java.base/java.lang.Class.forName0(Native Method)
	at java.base/java.lang.Class.forName(Class.java:413)
	at java.base/java.lang.Class.forName(Class.java:404)
	at groovy.grape.Grape.getInstance(Grape.java:124)
	at groovy.grape.Grape$1.run(Grape.java:161)
	at groovy.grape.Grape$1.run(Grape.java:158)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:319)
	at groovy.grape.Grape.grab(Grape.java:158)
	at groovy.grape.GrabAnnotationTransformation.visit(GrabAnnotationTransformation.java:380)
	at org.codehaus.groovy.transform.ASTTransformationVisitor.lambda$addPhaseOperationsForGlobalTransforms$5(ASTTransformationVisitor.java:374)
	at org.codehaus.groovy.control.CompilationUnit$ISourceUnitOperation.doPhaseOperation(CompilationUnit.java:897)
	at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:692)
	at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:666)
	at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:373)
	at groovy.lang.GroovyClassLoader.lambda$parseClass$2(GroovyClassLoader.java:316)
	at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
	at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
	at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
	at groovy.lang.GroovyShell.parseClass(GroovyShell.java:572)
	at groovy.lang.GroovyShell.parse(GroovyShell.java:585)
	at groovy.lang.GroovyShell.parse(GroovyShell.java:639)
	at groovy.lang.GroovyShell.parse(GroovyShell.java:643)
	at nextflow.script.ScriptParser.parse0(ScriptParser.groovy:175)
	at nextflow.script.ScriptParser.parse(ScriptParser.groovy:206)
	at nextflow.script.ScriptRunner.parseScript(ScriptRunner.groovy:229)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:136)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:372)
	at nextflow.cli.Launcher.run(Launcher.groovy:503)
	at nextflow.cli.Launcher.main(Launcher.groovy:657)
Caused by: java.lang.ClassNotFoundException: org.apache.ivy.util.MessageLogger
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:525)
	... 29 common frames omitted

Environment

• Nextflow version: v24.0.7.0-edge
• Java version: java 21.0.1 2023-10-17 LTS
• Operating system: Ubuntu
• Bash version: GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)

[pditommaso]

I think it's a side effect of the new launcher distribution. #3395

However, @Grab was never expected to be supported "officially" by nextflow. It's time to sunsetting it.

[VasLem]

I see, thank you for the answer, what is an alternative? I found no documentation about adding Groovy dependencies to a process, and Grape was really that it worked out of the box.

[bentsherman]

I would try moving this code into a Groovy script in the lib directory. If that doesn't work, I think you can also include a JAR file in the lib directory and it will be added to the classpath.

[bentsherman]

Docs: https://nextflow.io/docs/latest/sharing.html#utility-code

[VasLem]

Hi Ben, thanks for the input. Doesn't Google Batch require Tower in order to have the lib directory considered? If that's not the case, then including the jar file is a good enough alternative I guess.

[bentsherman]

The lib directory should work regardless of where you run your pipeline.