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:

  • AUGUSTUS - Ab-inito gene predictions
  • EvidenceModeler - Consensus gene build
  • PASA - Gene building using trancript information (RNAseq and/or ESTs)
  • MultiQC - Aggregate report describing results and QC from the whole pipeline
  • Pipeline information - Report metrics generated during the workflow execution

AUGUSTUS

Output files
  • annotations/augustus
    • *.augustus.gff: The gene build produced by AUGUSTUS in GFF3 format.
    • *.proteins.fa: The protein sequences corresponding to the AUGUSTUS gene build.
    • *.cdna.fa: The cDNA sequences corresponding to the AUGUSTUS gene build.
    • *.cds.fa: The CDS sequences corresponding to the AUGUSTUS gene build.

Evidence Modeler

Output files
  • annotations/evm
    • *.evm.gff: The gene build produced by EVM in GFF3 format.
    • *.proteins.fa: The protein sequences corresponding to the EVM gene build.
    • *.cdna.fa: The cDNA sequences corresponding to the EVM gene build.
    • *.cds.fa: The CDS sequences corresponding to the EVM gene build.

PASA

Output files
  • annotations/pasa
    • *.pasa.gff: The gene build produced by PASA in GFF3 format.
    • *.proteins.fa: The protein sequences corresponding to the PASA gene build.
    • *.cdna.fa: The cDNA sequences corresponding to the PASA gene build.
    • *.cds.fa: The CDS sequences corresponding to the PASA gene build.

RFam

Output files
  • annotations/ncrna
    • *.rfam.gff: Non-coding RNA preductions using RFam 14.

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.

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.