Introduction Usage Parameters Output

Introduction

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of 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.

Pipeline overview

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

  • Mislabels - Putative mislabels found by sativa-epang and raxtax
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

Mislabels

Output files
  • mislabels/
    • *.mislabels.tsv: putative mislabels, one row per flagged sequence, from sativa-epang and from the raxtax prefilter.

The table is tab-separated, with a header line and these columns:

Column Description
seq_name Sequence name
original_label Declared taxonomy, as a ;-separated lineage
predicted_label Taxonomy proposed by the method
lwr Confidence at the mismatching rank: sativa-epang’s Confidence, or the raxtax confidence
original_label_exclusion sativa-epang’s OriginalLabelExclusion: the placement weight outside the declared taxon at the mislabelled rank. NA for raxtax rows
mismatch_rank Rank where the lineages disagree, counted from the root (1 = first rank): the first differing rank for sativa, the checked rank for raxtax
method sativa or raxtax

A sativa-epang row with lwr 0.51 and original_label_exclusion near 1 is a stem placement: the sequence was placed on the branch between the proposed taxon and its parent. Sativa splits the weight of such a placement 0.49/0.51 between the two (a hardcoded value), so the 0.51 does not come from the data. The sequence is confidently outside its declared taxon, but it is not clear which neighbouring taxon it belongs to.

MultiQC

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.

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.

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