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genepi / nf-gwas

A nextflow pipeline to perform state-of-the-art genome-wide association studies.
https://genepi.github.io/nf-gwas
MIT License
63 stars 21 forks source link

'Nextflow.exit(int,String)' doesn't support array #90

Closed lindenb closed 9 months ago

lindenb commented 1 year ago

Hi, I got the following error message

Missing process or function exit([1, Parameter genotypes_prediction is required.])`

with stacktrace:

Caused by: groovy.lang.MissingMethodException: No signature of method: static WorkflowMain.exit() is applicable for argument types: (Integer, String) v
alues: [1, Parameter genotypes_prediction is required.]
Possible solutions: wait(), wait(long), wait(long, int), getAt(java.lang.String), grep(), dump()
        at groovy.lang.MetaClassImpl.invokeStaticMissingMethod(MetaClassImpl.java:1570)
        at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:1556)
        at org.codehaus.groovy.runtime.callsite.StaticMetaClassSite.callStatic(StaticMetaClassSite.java:62)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
(...)

using NF 23.10.0 .

it looks like Nextflow.exit https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy#L196 doesn't accept array/vector

seppinho commented 9 months ago

Thanks @lindenb. We already openend a pull request to fix this.

seppinho commented 9 months ago

Fixed by https://github.com/genepi/nf-gwas/pull/97