Nextflow is publishing output files in wrong directory

[henryone0910]

Bug report

My output files should be published in their right directory. But somehow, some of them was published in random directory.

Expected behavior and actual behavior

For instances, the syntax of a process is:
publishDir: "${params.outdir}/trimming", mode: 'copy'

Said that I have an example output:
output:
tuple val(sample), file("{sample}_trimmed_R1.fastq.gz"), file("{sample}_trimmed_R2.fastq.gz"), emit: trimmed_ch
I had 10 paired-end fastq samples as inputs for this process. Then it must publish 10 paired-end trimmed fastq to folder "trimming", as what we expected. But the actual result was that 9 output files were in their right destination, the remainder of them was published in somewhere in other process's directory.

Steps to reproduce the problem

The problem occured regardless of the first run or rerun.

Program output

I didn't have the problem of program output, nextflow often publish some files that didn't follow the pattern was set before.

Environment

• Nextflow version: 24.10.2
• Java version: openjdk 17.0.10-internal 2024-01-16
• Operating system: linux system.
• Bash version: (use the command $SHELL --version)
  GNU bash, version 4.4.20(1)-release (x86_64-redhat-linux-gnu)

Additional context

(Add any other context about the problem here)

[bentsherman]

Can you provide a minimal reproducible example?