WGS Nextflow Pipeline

(nf-wgs-dsl2)

Adapted from:

• https://github.com/Karaniare/Optimized_GATK4_pipeline (shell script)
• https://github.com/jhoneycuttr/nf-wgs (Nextflow DSL 1)

Documentation, please refer to: https://eppicenter.github.io/nf-wgs-dsl2/

Overview

• main.nf: WGS workflow
• nextflow.config: config file
• workflows
  • qc.nf: QC sub-workflow
  • gvcf.nf: GVCF sub-workflow
• config
  • Apptainer: file used to build nf-wgs-dsl2.sif
  • Dockerfile: file for building docker image
  • base.config: base config file
  • envs: conda envs (under construction 🚧)
• refs: reference files used by both QC_workflow and gVCF_workflow
  • adapters: folder containing trimmomatic adapter files
  • genomes: reference genome files and more
  • run_quality_report.Rmd: r script for quality report used in QC_workflow
• data: suggested directory for input files
• results: suggested directory for output

Parameters

nextflow.config

Parameters	Description
qc_only	If enabled, only QC workflow is run (default 'false')
gvcf_only	If enabled, only gVCF workflow is run (default 'false')
inputdir	The folder that contains the input files (default 'data')
outputdir	The folder where you want the resulting data to be save (default 'results/results')
trimadapter	The adapter used for initial trimming of reads (default 'NexteraPE-custom.fa')