Thanks @Adam_Talbot, here’s more about my code and I believe I’ve used mostly like you recommended.
The thing is, in my original nextflow.config, I was trying to dynamically assign a pattern name for the results.
I can’t figure out how to do it without env. But I haven’t considered file instead of new File, I’m gonna give a try:
env {
trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
input_name = file(params.input).name
}