jtmccr1 / nf-core-phylofunk

An nf-core compatible pipeline for running BEAST analysis

This pipeline is used to help coordinate phylogeographic analysis of large viral datasets focusing on Sars-CoV-2.

Introduction

nf-core/phylofunk is a bioinformatics best-practise analysis pipeline for

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

1. Install nextflow (>=20.04.0)

2. Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run nf-core/phylofunk -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>

   Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run nf-core/phylofunk -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37

See usage docs for all of the available options when running the pipeline.

Pipeline Summary

By default, the pipeline currently performs the following:

• Sequencing quality control (FastQC)
• Overall pipeline run summaries (MultiQC)

Documentation

The nf-core/phylofunk pipeline comes with documentation about the pipeline: usage and output.

Credits

nf-core/phylofunk was originally written by JT McCrone.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

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

Citations

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

In addition, references of tools and data used in this pipeline are as follows: