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nf-core / demultiplex

Demultiplexing pipeline for sequencing data
https://nf-co.re/demultiplex
MIT License
44 stars 37 forks source link

Remove adapter code doesnt work in all cases #260

Closed apeltzer closed 1 month ago

apeltzer commented 1 month ago

I found that this here:

https://github.com/nf-core/demultiplex/blob/17cde5d8f22f5327beac9637e941e4775ada1b3f/workflows/demultiplex.nf#L73-L82

Doesnt work all the time with all samplesheets. Particularly i had one with single cell data that caused an error like this:

Sep-12 15:38:25.444 [Actor Thread 32] ERROR nextflow.extension.OperatorImpl - @unknown
**java.lang.IndexOutOfBoundsException: index is out of range 0..-1 (index = 0)**
    at org.codehaus.groovy.runtime.StringGroovyMethods.getAt(StringGroovyMethods.java:1373)
    at org.codehaus.groovy.runtime.dgm$1263.doMethodInvoke(Unknown Source)
    at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
    at Script_d620b82475db33ec$_runScript_closure1$_closure2$_closure4.doCall(Script_d620b82475db33ec:80)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
    at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
    at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
    at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
apeltzer commented 1 month ago

Looks like its a problem when we don't add a lane (e.g. want to demux all lanes).

nschcolnicov commented 1 month ago

Created a PR for this: https://github.com/nf-core/demultiplex/pull/265