In some cases PublishDir throws a FileAlredyExistsException

[pditommaso]

Stack trace

ERROR nextflow.processor.TaskProcessor - Error executing process > '_6_bwa_align (1)'

Caused by:
  /home/pditommaso/projects/singularity-scientific-example/output/_6_bwa_align/container.bam

java.nio.file.FileAlreadyExistsException: /home/pditommaso/projects/singularity-scientific-example/output/_6_bwa_align/container.bam
	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:88)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
	at sun.nio.fs.UnixFileSystemProvider.createSymbolicLink(UnixFileSystemProvider.java:456)
	at java.nio.file.Files.createSymbolicLink(Files.java:996)
	at nextflow.processor.PublishDir.processFileImpl(PublishDir.groovy:303)
	at nextflow.processor.PublishDir.processFile(PublishDir.groovy:294)
	at nextflow.processor.PublishDir.apply(PublishDir.groovy:237)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:923)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:906)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:74)
	at nextflow.processor.PublishDir$_apply_closure1.doCall(PublishDir.groovy:216)
	at nextflow.processor.PublishDir$_apply_closure1.call(PublishDir.groovy)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2030)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2015)
	at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2056)
	at nextflow.processor.PublishDir.apply(PublishDir.groovy:215)
	at nextflow.processor.TaskProcessor.publishOutputs(TaskProcessor.groovy:1205)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at nextflow.processor.TaskProcessor.finalizeTask0(TaskProcessor.groovy:1980)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:210)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:166)
	at nextflow.processor.TaskProcessor.finalizeTask(TaskProcessor.groovy:1951)
	at nextflow.processor.TaskPollingMonitor.checkTaskStatus(TaskPollingMonitor.groovy:438)
	at nextflow.processor.TaskPollingMonitor.checkAllTasks(TaskPollingMonitor.groovy:394)
	at nextflow.processor.TaskPollingMonitor.pollLoop(TaskPollingMonitor.groovy:340)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93)
	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1215)
	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1024)
	at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:923)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:906)
	at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:74)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.doCall(TaskPollingMonitor.groovy:319)
	at nextflow.processor.TaskPollingMonitor$_start_closure6.call(TaskPollingMonitor.groovy)
	at groovy.lang.Closure.run(Closure.java:495)
	at java.lang.Thread.run(Thread.java:745)

[pditommaso]

Fixed in 0.23.3.