Hello, I am trying to run the pipeline with the --trim_nextseq option. In Usage, the parameter is supposed to be a string, which does not make sense to me. The nf-core rnaseq 3.1 pipeline also uses the TrimGalore Module and the parameter type for the same option --trim_nextseq is an integer. nextflow run nf-core/metatdenovo -r 2.0.0 -profile singularity --input samplesheet.csv --trim_nextseq '20' Error: --trim_nextseq (20): Value is [integer] but should be [string] Thank you for your help!

Hi! Thanks for the report: you're right there is a bug here.

--trim_nextseq

was declared as

string

in the schema even though it's used numerically internally. A fixed in PR #598 is on it's way but for now you can try a work around it by setting

trim_nextseq

via a config file instead of

--trim_nextseq

on the command line (config-file values aren't subject to the CLI string-typing check that was rejecting it).

Thank you so much! I will try the work around.

Make sure it's a parameter file and not a nextflow config, see nf-co.re/docs/…/create-params-file