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phac-nml/cditoxins: 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.

  • blastn: very small mock assembly files for each sample
  • pipeline_info: information about the pipeline's execution

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:

  • Make BLASTdb - Makes a nucleotide blast database from the reference toxin genes
  • BLASTN - Runs a blast search with the query genome assemblies against the reference gene database
  • Filtering blast - Filters the output blast results to get positive/negative values for each toxin target
  • IRIDA Next Output - Generates a JSON output file that is compliant with IRIDA Next
  • Pipeline information - Report metrics generated during the workflow execution

Make BLASTdb

Output files
  • None

BLASTN

Output files
  • /
    • If one or more samples had an assembly size of zero, a text file containing a list of empty assemblies and were not evaluated by blastn for toxin genes: errors.csv
    • If one or more samples had no hits in blastn, a text file containing list of samples that had no hits: nohits.csv
  • blastn/
    • Text files: SAMPLEID.txt

Filtering blast

Output files
  • /
    • Text summary describing samples and toxin results: results.csv
      • NEG indicates no toxin gene detected
      • POS indicates a toxin gene was detected
      • POSDEL indicates a toxin gene with a previously described deletion was detected
      • NaN indicates the sample/toxin was not evaluated due to empty assembly

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.