Introduction## 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.

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: QUILT imputation mode

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

Glimpse Chunk

  • quilt_impute/glimpse/
    • *.txt: TXT file containing the chunks obtained from running Glimpse chunks.

Glimpse chunk defines chunks where to run imputation. For further reading and documentation see the Glimpse documentation. Once that you have generated the chunks for your reference panel, you can skip the reference preparation step and directly submit this file for imputation.

Convert

  • quilt_impute/bcftools/convert/
    • *.hap: a .hap file for the reference panel.
    • *.legend*: a .legend file for the reference panel.

bcftools aids in the conversion of vcf files to .hap and .legend files. A .samples file is also generated. Once that you have generated the hap and legend files for your reference panel, you can skip the reference preparation step and directly submit these files for imputation (to be developed).

QUILT

  • quilt_impute/quilt/
  • quilt.*.vcf.gz: Imputed VCF for a specific chunk.
  • quilt.*.vcf.gz.tbi: TBI for the Imputed VCF for a specific chunk.

quilt performs the imputation. This step will contain the VCF for each of the chunks.

Concat

  • quilt_impute/bcftools/concat
  • .*.vcf.gz: Imputed and ligated VCF for all the input samples.

bcftools concat will produce a single VCF from a list of imputed VCFs in chunks.

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. 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.