The process CREATE_ANNDATA_MUDATA seems to start even though I set:

--generate_mudata false --generate_anndata false

Thanks for pointing that out. That’s a remnant of the legacy pipeline. I hadn’t planned on keeping that option. I’ll remove the parameters. You should still be able to suppress the process using

-c custom.config

. `custom.config`:

process {
     withName: 'CREATE_ANNDATA_MUDATA' {
         enabled = false
     }
}

Somehow that didn't work for me either