Home

PughLab pipeline-suite (version 0.4.1)

Introduction

This is a collection of pipelines to be used for NGS (both DNA and RNA) analyses, from alignment to variant calling.

Start by creating a clone of the repository:

cd /path/to/some/directory
git clone https://github.com/pughlab/pipeline-suite/

Additionally, the report generation portion of this tool requires installation of the BPG plotting package for R: https://CRAN.R-project.org/package=BoutrosLab.plotting.general

Set up config files

There are example config files located in the "configs" folder:

• data configs:

  • fastq_dna_config.yaml and fastq_rna_config.yaml, can be generated using create_fastq_yaml.pl, however this is dependent on filenames being in the expected format (otherwise, just copy the examples!)
  • bam_config.yaml, generated by any tool which outputs BAMs that are required for downstream steps

• pipeline configs (dna_pipeline_config.yaml and rna_pipeline_config.yaml):

  • these specify common parameters, including:
    • project name
    • sequencing type (wgs, exome, rna or targeted), sequencing center and platform
    • path to desired output directory (will be created if this is the initial run)
    • paths to tool-specific reference files/directories and ref_type (hg19 or hg38)
    • desired versions of tools
    • for each tool, memory and run time parameters for each step