Hello, I am new to the community, so please feel free to help me get to the right place if this is not it. I am running the rnaseq workflow and have added

--chimSegmentMin 10

to the

"extra_star_align_args"

setting. This causes STAR to generate a

*.Chimeric.out

output file for each sample, but these files remains in the work directory upon workflow completion. What is the correct way for me to handle this as an end-user if I would like these files to be published into the

outdir

folder along with the other output files from STAR?

You will need to modify the configuration of this process and add a publishDir directive that comprises the

*.Chimeric.out

files.

Thanks Matthias! I was not aware that one could use configuration to make changes to

publishDir

that way; but it makes sense now that you suggest it. I’ll try this out.