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nf-cmgg/germline

Introduction

nf-cmgg/germline is a nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

Pipeline summary

metro graph

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Quick Start

  1. Install Nextflow (>=24.10.0)
  2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).
samplesheet.csv
sample,family,cram,crai
SAMPLE_1,FAMILY_1,SAMPLE_1.cram,SAMPLE_1.crai

Each row represents a single sample to be analysed. More information can be found in the usage documentation.

Now, you can run the pipeline using:

nextflow run nf-cmgg/germline --input samplesheet.csv --outdir <OUTDIR> --genome GRCh38 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

This pipeline contains a lot of parameters to customize your pipeline run. Please take a look at the parameters documentation for an overview.

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

nf-cmgg/germline was originally written and is maintained by @nvnieuwk.

Special thanks to @matthdsm for the many tips and feedback and to @mvheetve and @ToonRossel for testing the pipeline.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references can be found in the CITATIONS section.