output.md

ferlab/postprocessing: Output

Introduction

This document describes the output produced by the pipeline. The directories listed below will be created in the output directory after the pipeline has finished. All paths are relative to the top-level output directory.

Pipeline overview

Pipeline information

Output files

• pipeline_info/
  • Reports generated by nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.html.
  • Parameters used by the pipeline run: params.json.
  • A copy of the nextflow log file: nextflow.log. Note that it will miss logs written after the workflow.onComplete handler is run.
  • Copies of the configuration files used: config/*.config. This includes the default nextflow.config file as well as any additional configuration files passed as parameters.
  • Other metadata relevant for reproducibility: metadata.txt . It contains information such as the original command line, the name of the branch and revision used, the username of the person who submitted the job, a list of configuration files passed, the nextflow work directory, etc.
• splitmultiallelics/: pipeline output before running the tools specified via the tools parameter.
• vep/: vep output
• exomiser/results: exomiser output

You might see other folders named after different pipeline processes. These are considered intermediate pipeline outputs.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.