Hey, I am reviewing the new rnastructurome pipeline (github.com/nf-core/rnastructurome), and am not sure if this is a valid way to organise the main.nf (hopefully its fine). But the pipeline allows all columns in a samplesheet to be filled in by params given at command line. E.g. Organism, if not set in the samplesheet, then adding --organism ‘Homo sapiens’, will use that for all samples in the sheet. github.com/nf-core/rnastructurome/pull/5/changes#… It is set in a subworkflow. So that if there is content in the samplesheet for a particular attribute the param will not overwrite it. It only overides with a param if the field is empty. rnastructurome/subworkflows/local/utils_nfcore_rnastructurome_pipeline/main.nf at 2678cdd9f6a82c25d6… Not sure if this is a useful feature, but if it is, is this allowed in an nf-core pipeline?

As far as i know this is fine, i am doing the same in genomassembler

OK, cool, good to know! Thanks