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

assemblerflow.templates.pipeline_status.get_json_info(fields, header)[source]
Parameters:
fields
assemblerflow.templates.pipeline_status.get_previous_stats(stats_path)[source]
Parameters:
workdir
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