output.md

phac-nml/iridanextexample: Output

Introduction

This document describes the output produced by the pipeline.

The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

• assembly: very small mock assembly files for each sample
• generate: intermediate files used in generating the IRIDA Next JSON output
• pipeline_info: information about the pipeline's execution
• simplify: simplified intermediate files used in generating the IRIDA Next JSON output
• summary: summary report about the pipeline's execution and results

The IRIDA Next-compliant JSON output file will be named iridanext.output.json.gz and will be written to the top-level of the results directory. This file is compressed using GZIP and conforms to the IRIDA Next JSON output specifications.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• Assembly stub - Performs a stub assembly by generating a mock assembly
• Generate sample JSON - Generates a JSON file for each sample
• Generate summary - Generates a summary text file describing the samples and assemblies
• Simplify IRIDA JSON - Simplifies the sample JSONs by limiting nesting depth
• IRIDA Next Output - Generates a JSON output file that is compliant with IRIDA Next
• Pipeline information - Report metrics generated during the workflow execution

Assembly stub

Output files

• assembly/
  • Mock assembly files: ID.assembly.fa.gz

Generate sample JSON

Output files

• generate/
  • JSON files: ID.json.gz

Generate summary

Output files

• summary/
  • Text summary describing samples and assemblies: summary.txt.gz

Simplify IRIDA JSON

Output files

• simplify/
  • Simplified JSON files: ID.simple.json.gz

IRIDA Next Output

Output files

• /
  • IRIDA Next-compliant JSON output: iridanext.output.json.gz

Pipeline information

Output files

• pipeline_info/
  • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
  • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline.
  • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.
  • Parameters used by the pipeline run: params.json.

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.