output.md

phac-nml/staramrnf: Output

Introduction

This document describes the output produced by the pipeline.

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

.
├── csvtk
├── pipeline_info
└── staramr

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:

• AMR Bacterial Scans - Scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases and compiles a summary report of detected antimicrobial resistance genes.
• Pipeline information - Report metrics generated during the workflow execution

AMR Bacterial Scans

Output files

• staramr/
  • StarAMR search results for each sample:
    • sample_detailed_summary.staramr.tsv
    • sample_mlst.staramr.tsv
    • sample_plasmidfinder.staramr.tsv
    • sample_pointfinder.staramr.tsv (Pointfinder organisms)
    • sample_resfinder.staramr.tsv
    • sample_results.staramr.xlsx
    • sample_settings.staramr.txt
    • sample_summary.staramr.tsv
• csvtk/
  • Combine results from all samples into a single report
    • merged_detailed_summary.staramr.tsv
    • merged_mlst.staramr.tsv
    • merged_plasmidfinder.staramr.tsv
    • merged_pointfinder.staramr.tsv (Pointfinder organisms)
    • merged_resfinder.staramr.tsv
    • merged_summary.staramr.tsv

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.