Workflow output with file publish targets causes NullPointerException #6340
Description
Bug report
Expected behavior and actual behavior
Trying out the new Workflow outputs (third preview version). I'm attempting to reproduce publishDir behavior, where individual files from process outputs can be renamed.
The correct published outputs are generated successfully, but then immediately afterwards there was a NPE. Not sure if it's related but I think it is, because when I redefine the output directive more simply, the NPE doesn't happen.
Steps to reproduce
process multiqc {
// ...
output:
tuple val(srr), path('multiqc_report.html'), path('multiqc_data/multiqc_data.json'), path('multiqc_data/multiqc_fastqc.txt')
// ...
}
workflow {
main:
// ...
publish:
mqc = multiqc.out
}
output {
mqc {
path { srr, report, data_json, fastqc_txt ->
report >> "02.multiQC/${srr}_report.html"
data_json >> "02.multiQC/${srr}_data.json"
fastqc_txt >> "02.multiQC/${srr}_fastqc.txt"
}
}
}Program output
Aug-12 14:26:56.087 [Actor Thread 12] ERROR nextflow.extension.DataflowHelper - @unknown
java.lang.NullPointerException: null
at java.base/java.util.Objects.requireNonNull(Objects.java:220)
at java.base/sun.nio.fs.UnixFileSystem.getPath(UnixFileSystem.java:296)
at java.base/java.nio.file.Path.resolve(Path.java:516)
at nextflow.extension.PublishOp$_getTargetDir_closure1.doCall(PublishOp.groovy:144)
at nextflow.extension.PublishOp$_getTargetDir_closure1.call(PublishOp.groovy)
at nextflow.extension.PublishOp.normalizePath(PublishOp.groovy:308)
at nextflow.extension.PublishOp.access$0(PublishOp.groovy)
at nextflow.extension.PublishOp$_normalizePaths_closure2.doCall(PublishOp.groovy:269)
at nextflow.extension.PublishOp$_normalizePaths_closure2.call(PublishOp.groovy)
Environment
- Nextflow version: 25.04.6 build 5954
- Java version: openjdk 23.0.2
- Operating system: Linux
- Bash version: 4.2 (zsh 5.0.2)
Additional context
(Add any other context about the problem here)