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:

Generate-Accessories

Output files
  • accessoriy_files/
    • coverage.bigWig: Graph file containing coverage data. For Pretext ingestion.
    • logcoverage.bigWig: Graph file containing coverage data. For Pretext ingestion.
    • halfcoverage.bigWig: Graph file containing coverage data where coverage is equal to half the max.
    • maxcoverage.bigWig: Graph file containing coverage data where coverage is max.
    • *_gap.bedgraph: Bed graph with locations of gaps in the sequence. For Pretext ingestion.
    • *_telomere.bed: Bed file containing telomeric motif site.
    • *_telomere.bedgraph: Bed graph with locations of telomeric motif. For Pretext ingestion.
    • *_repeat_density.bigWig: Graph file containing relative repeat density across the genome. For Pretext ingestion.

The accessory files are generated in the ALL_FILES sub workflow, and are generated in order to be ingested into the pretext files which is detailed on the pipelines website.

Generate-Maps

Output files
  • pretext_maps_raw/
    • hic_hr.pretext: A Hi-Res pretext file generated by PretextMap.
    • hic_normal.pretext: The standard pretext file generated by PretextMap.
    • hic_normalFullMap.png: A static image of the normal.pretext file.

These files are always generated by the pipeline and viewed in PretextView (a gui for pretext map manipulation). As the viewing of the pretext files can be memory intensive to load, we also generate a png for a quick glance. These now by default have the accessory files embedded into the pretext file.

Processed Pretext

Output files
  • pretext_maps_processed/
    • hic_hr.pretext: A Hi-Res pretext file generated by PretextMap.
    • hic_normal.pretext: The standard pretext file generated by PretextMap.

These files will have the accessory files ingested into them

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.