Hi,
I found a bug in nextflow v25.04.3.

I get these errors in the log of many processes:

cp: '.command.out' and '/scratch/analysis/work/61/9a68b6a99e3766137c31971f72db9a/.command.out' are the same file
cp: '.command.err' and '/scratch/analysis/work/61/9a68b6a99e3766137c31971f72db9a/.command.err' are the same file

The cp commands in the .command.run script are doing this. Not sure why.

Note, there are no other errors in the process log and all the output files were made ok.