GEMmaker no longer creates nextflow reports by default

[JohnHadish]

Description of feature

GEMmaker used to automatically produce the summary, timeline, and trace reports by default. The user must now request these to be run manually.

GEMmaker Documentation on Reports
Nextflow Documentation

What needs to be added back in:

trace {
    enabled = true
    file = 'pipeline_trace.txt'
    fields = 'task_id,name,status,exit,realtime,%cpu,rss'
}

[spficklin]

I recently ran GEMmaker and got these files in the results/pipeline_info directory:

execution_report_2022-11-06_16-53-56.html    
execution_trace_2022-11-06_16-53-56.txt
execution_timeline_2022-11-06_16-53-56.html  
pipeline_dag_2022-11-06_16-53-56.svg

Are these the files you are missing?

[JohnHadish]

Yes, those are the missing files. Do you have your submission script for that run?

[spficklin]

Yes, I do. I'll send them to you. I didn't include the trace settings above.