How can I set paths relative to the project dir in

nextflow_schema.json

? Whey I run

nf-core piplines schema build

, it updates all paths that use

${projectDir}

into absolute paths in

nextflow_schema.json

, although that is obviously not desirable.

What's the use case? The schema doesn't normally reference files in the project directory

We are referring to some assets (database files) in the project folder.

A good workaround would be to host the files on the pipeline branch in test-datasets. The schema is not a Nextflow file, so the magic variable will probably not work. I'm not sure relying on env variables is good either.

Thank you for the input! Will see how far I get with the current workaround, but yea, we will probably need to revisit this to set things up in a more best practice way!

See this thread: https://nfcore.slack.com/archives/CE5LG7WMB/p1742998273284579?thread_ts=1742996506.321399&cid=CE5LG7WMB It seems to be ignored. At least that appears to be how nf-core/rnaseq does it

@Mahesh Binzer-Panchal Ah, yes, definitely seems to make sense to ignore. Thank you!