I have an issue with rnaseq pipeline. When adding " --remove_ribo_rna, --use_gpu_ribodetector, --use_parabricks_star" I get the following error: ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details The following invalid input values have been detected: * --remove_ribo_rna (true): Value is [string] but should be [boolean] * --use_gpu_ribodetector (true): Value is [string] but should be [boolean] * --use_parabricks_star (true): Value is [string] but should be [boolean] I have tried numerous ways to convert these parameters to boolean but none of them have worked. Any advice would be welcome. Thank you!. Otherwise, the rnaseq pipeline has been very helpful to me, thank you for putting so much effort into the design and making it work!

Can you provide the actual command you used? I assume you're not actually putting

,

on the command line?

I suspect it may have something to do with the fact that parameters now automatically have type

string

assigned to them in the newest Nextflow versions. Are you actually putting

true

after each parameter? If so, have you tried without doing that? (It is valid syntax -- but not required, since it is the default if you use the option -- to specify

true

.) You can also try an older Nextflow version, 25.10.x. -- e.g.

NXF_VER=25.10.4 nextflow run ...

. That would confirm that it is a problem with the new typing if it works.

Had the same problem with another pipeline and solved it by providing boolean parameters in a separate params.json file like:

{
  "save_reference": true
}

and run like

nextflow run nf-core/pipeline -params-file params.json ...

Yes, JSON file entries have a defined type (e.g.

true

is boolean,

"true"

is a string), so the assumption that everything is a string does not apply like it does for parameters.

I was able to solve this issue by providing the boolean parameters from the config file instead of adding them to the terminal command. I did put

true

after each parameter in the terminal, it is weird that this behaves this way.

Think I fixed it actually: https://github.com/nf-core/rnaseq/pull/1864 Maybe someone could test for me off the branch?

My feedback about the "Value is [string] but should be [boolean]" errors - I just tried running nf-core/rnaseq 3.27.0. It requested nextflow verison >=25.10.4; the only suitable module available on our HPF was nextflow 26.04.6. When I provided boolean arguments on the nextflow run nf-core/rnaseq command line just as "--gencode " I had "Value is [string] but should be [boolean]" errors. When I added all boolean options to a json file, the pipeline moved past the error point and is running now.