Introduction Usage Parameters Output Releases

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 repaired subfolder of the output folder set up using the --outdir command line parameter.

<output folder>
  - pipeline_info/
  - QC/
    - fastqc/
    - fq_lint/
    - multiqc/
  - repaired/
  - repaired_samplesheet.csv
Folders content
  • pipeline_info contains report metrics generated during the workflow execution
  • QC contains the fq lint status of the samples, FastQC QC analysis results and MultiQC reports
  • repaired contains the fastq files of all the samples and the quality reports of the repaired ones
    • mysampleA_1.fastq.gz (and mysampleA_2.fastq.gz) are the repaired fastq files of a paired-end sample, mysampleC.fastq.gz that of a single-end sample
    • mysampleA_1.report (and mysampleA_2.report) are the summaries of the cleaning task
    • the samples that passed fq lint were not repaired: their reads are only copied here (compressed, if they were not), with the same names and without a report
  • repaired_samplesheet.csv is the samplesheet of the reads in repaired

fq lint

Unless --skip_fq_lint is used, the input reads are checked with fq lint before anything else. The samples that pass the check are not repaired, which saves the repair of large files that are fine. A sample is only skipped when its fq lint log looks clean: if the check fails or cannot run, the sample is repaired as usual. Skipped samples still get a FastQC and a MultiQC report.

Output files
  • QC/fq_lint/
    • fq_lint_status_mqc.tsv: for each sample, whether it passed or failed fq lint (also failed if the check could not run) and whether the repair was skipped or run. The table is also shown in the MultiQC report.

Repaired samplesheet

repaired_samplesheet.csv lists the samples in repaired in the samplesheet format of this pipeline and of other nf-core pipelines, so that the repaired reads can be given as --input to a downstream pipeline. Samples without any reads left, because all their reads were empty or could not be recovered, are not listed.

repaired_samplesheet.csv
sample,fastq_1,fastq_2
mysampleA,<output folder>/repaired/mysampleA_1.fastq.gz,<output folder>/repaired/mysampleA_2.fastq.gz
mysampleC,<output folder>/repaired/mysampleC.fastq.gz,

FastQC

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.

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.

MultiQC

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.

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.

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.

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