While testing the pipeline, I noticed that the project_celltype_metafile parameter is missing from the schema json file.
I re-ran nf-core schema build, and it still didn't end up in the json. I wondered if this is because this parameter is only defined in config/profile_ccdl.config. So, I added project_celltype_metafile = "celltype_metadata.tsv" into nextflow.config to test out the theory. Indeed when I next ran nf-core schema build, I was prompted:
✨ Found 'params.project_celltype_metafile' in the pipeline config, but not in the schema. Add to pipeline schema? [y/n]:
It's worth checking if there are other parameters that are in a similar situation and then addressing them consistently.
While testing the pipeline, I noticed that the
project_celltype_metafileparameter is missing from the schema json file.I re-ran
nf-core schema build, and it still didn't end up in the json. I wondered if this is because this parameter is only defined inconfig/profile_ccdl.config. So, I addedproject_celltype_metafile = "celltype_metadata.tsv"intonextflow.configto test out the theory. Indeed when I next rannf-core schema build, I was prompted:It's worth checking if there are other parameters that are in a similar situation and then addressing them consistently.