Introduction Usage Parameters Output

Introduction

This document describes the output produced by 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.

{outdir}
โ”œโ”€โ”€ bootstrapping
โ”‚   โ”œโ”€โ”€ round_1
โ”‚   โ”‚   โ”œโ”€โ”€ bqsr
โ”‚   โ”‚   |   โ”œโ”€โ”€ cram
|   |   |   |   โ””โ”€โ”€ merged
โ”‚   โ”‚   |   โ””โ”€โ”€ qc
|   |   โ”œโ”€โ”€ stats
โ”‚   โ”‚   โ””โ”€โ”€ variants
โ”‚   โ”‚       โ”œโ”€โ”€ db
โ”‚   โ”‚       โ”œโ”€โ”€ filtered
โ”‚   โ”‚       โ””โ”€โ”€ merged
|   |
โ”‚   โ”œโ”€โ”€ round_2
โ”‚   โ”‚   โ”œโ”€โ”€ โ€ฆ
|   โ‹ฎ    โ‹ฎ
|   โ‹ฎ
โ”‚   โ””โ”€โ”€ round_3
โ”‚       โ”œโ”€โ”€ โ€ฆ
|       โ‹ฎ
|
โ”œโ”€โ”€ intervals
|
โ”œโ”€โ”€ multiqc
|
โ”œโ”€โ”€ pipeline_info
|
โ”œโ”€โ”€ preprocessing
โ”‚   โ”œโ”€โ”€ alignment
|   |    โ”œโ”€โ”€ bam
โ”‚   |    โ””โ”€โ”€ cram
|   |
โ”‚   โ”œโ”€โ”€ coverage
โ”‚   โ”œโ”€โ”€ fastp
โ”‚   โ”œโ”€โ”€ preseq
โ”‚   โ””โ”€โ”€ stats
|
โ”œโ”€โ”€ variant_calling
โ”‚   โ”œโ”€โ”€ bcftools
|        โ”œโ”€โ”€ merged
โ”‚   |    โ””โ”€โ”€ bam
|   |
โ”‚   โ””โ”€โ”€ gatk
|        โ”œโ”€โ”€ I<interval>_joint
|        โ‹ฎ
|        โ”œโ”€โ”€ merged
โ”‚        โ””โ”€โ”€ stats
|
โ””โ”€โ”€ relatedness_estimation
    โ”œโ”€โ”€ exclude
    |
    โ”œโ”€โ”€ intersection
    |
    โ”œโ”€โ”€ thinned
    |
    โ”œโ”€โ”€ <tool1>
    |
    โ””โ”€โ”€ <tool2>
work/
.nextflow.log

Pipeline overview

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

Preprocessing

Prepare Reference Genome

Prepare Intervals

Prepare Input Files

Map to Reference

Mark Duplicates

Bootstrapping

Call Variants

Hard Filter Variants

Base Quality Score Recalibration

Variant Calling

Relatedness Estimation

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 parameterโ€™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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