Introduction Usage Parameters Output

Introduction

This document describes the output produced by the pipeline.

Pipeline overview

The nf-core/fastqrepair pipeline is built using Nextflow. Output files are gathered into the pickup subfolder of the output folder set up using the --outdir command line parameter.

-- <output folder>
    |
    pickup/
      |
      - mysampleA_R1_repaired.fastq.gz
      - mysampleA_R2_repaired.fastq.gz
      - mysampleA_R1_report.txt
      - mysampleA_R2_report.txt
      |
      QC/
        - mySampleA_1_fastqc.html
        - mysampleA_1_fastqc.zip
        - mySampleA_2_fastqc.html
        - mysampleA_2_fastqc.zip
      |
      pipeline_info/
        - execution_report.html
        - execution_timeline.html
        - execution_trace.txt
        - params.json
        - pipeline_dag.html
        - nf-core_fastqrepair_versions.yml

where

  • mysampleA_R1_repaired.fastq.gz and mysampleA_R2_repaired.fastq.gz are the repaired fastq files
  • mysampleA_R1_report.txt and mysampleA_R2_report.txt are the summaries of the cleaning task by FastqWiper
  • QC contains FastQC QC analysis results
  • pipeline_info contains report metrics generated during the workflow execution

FastqWiper

Output files
  • pickup/
    • mysampleA_R1_report.txt: a textual file that contains the results of the cleaning tasks of FastqWiper for read R1.
    • mysampleA_R2_report.txt: a textual file that contains the results of the cleaning tasks of FastqWiper for read R2.
  • FastQC - Raw read QC- MultiQC - Aggregate report describing results and QC from the whole pipeline
  • FastqWiper is a Python package that makes an uncompliant FASTQ file well-formed by dropping and fixing pesky lines.
  • Pipeline information - Report metrics generated during the workflow execution

FastQC

Output files
  • fastqc/
    • *_fastqc.html: FastQC report containing quality metrics.
    • *_fastqc.zip: Zip archive containing the FastQC report, tab-delimited data file and plot images.

FastQC gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the FastQC help pages.### 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.html.
    • 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.