assemblerflow.templates.pipeline_status module¶
Purpose¶
This module is intended to collect pipeline run statistics (such as time, cpu, RAM for each tasks) into a report JSON
Expected input¶
trace_file
: Trace file generated by nextflow
Code documentation¶
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assemblerflow.templates.pipeline_status.
main
(fastq_id, trace_file, workdir)[source]¶ Parses a nextflow trace file, searches for processes with a specific tag and sends a JSON report with the relevant information
The expected fields for the trace file are:
0. task_id 1. process 2. tag 3. status 4. exit code 5. start timestamp 6. container 7. cpus 8. duration 9. realtime 10. queue 11. cpu percentage 12. memory percentage 13. real memory size of the process 14. virtual memory size of the process
Parameters: - trace_file : str
Path to the nextflow trace file