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nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
128 stars 78 forks source link
adna ancient-dna-analysis ancientdna bioinformatics genome metagenomics nextflow nf-core pathogen-genomics pipeline population-genetics workflow

readme

nf-core/eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

GitHub Actions CI Status GitHub Actions Linting Status Nextflow nf-core DOI Published in PeerJ

install with bioconda Docker Singularity Container available

Get help on Slack

[!IMPORTANT]
nf-core/eager versions 2.* are only compatible with Nextflow versions up to 22.10.6!

Introduction

nf-core/eager is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.

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. The pipeline pre-processes raw data from FASTQ inputs, or preprocessed BAM inputs. It can align reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making installation trivial and results highly reproducible.

nf-core/eager schematic workflow

Quick Start

  1. Install nextflow (>=20.07.1 && <=22.10.6)

  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/eager -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/eager -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --fasta '<your_reference>.fasta'

  5. Once your run has completed successfully, clean up the intermediate files.

    nextflow clean -f -k

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

N.B. You can see an overview of the run in the MultiQC report located at ./results/MultiQC/multiqc_report.html

Modifications to the default pipeline are easily made using various options as described in the documentation.

Pipeline Summary

Default Steps

By default the pipeline currently performs the following:

Additional Steps

Additional functionality contained by the pipeline currently includes:

Input

Preprocessing

aDNA Damage manipulation

Genotyping

Biological Information

Metagenomic Screening

Functionality Overview

A graphical overview of suggested routes through the pipeline depending on context can be seen below.

nf-core/eager metro map

Documentation

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

  1. Nextflow installation
  2. Pipeline configuration
  3. Running the pipeline
    • This includes tutorials, FAQs, and troubleshooting instructions
  4. Output and how to interpret the results

Credits

This pipeline was mostly written by Alexander Peltzer (apeltzer) and James A. Fellows Yates, with contributions from Stephen Clayton, Thiseas C. Lamnidis, Maxime Borry, Zandra Fagernäs, Aida Andrades Valtueña and Maxime Garcia and the nf-core community.

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

Authors (alphabetical)

Additional Contributors (alphabetical)

Those who have provided conceptual guidance, suggestions, bug reports etc.

If you've contributed and you're missing in here, please let us know and we will add you in of course!

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #eager channel (you can join with this invite).

Citations

If you use nf-core/eager for your analysis, please cite the eager preprint as follows:

Fellows Yates JA, Lamnidis TC, Borry M, Valtueña Andrades A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947. DOI: 10.7717/peerj.10947.

You can cite the eager zenodo record for a specific version using the following doi: 10.5281/zenodo.3698082

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:

Data References

This repository uses test data from the following studies: