Introduction

sanger-tol/ensemblgenedownload is a pipeline that downloads gene annotations from Ensembl into the Tree of Life directory structure.

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!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the GitHub CI infrastructure. This ensures that the pipeline runs in a third-party environment, and has sensible resource allocation defaults set to run on real-world datasets.

Pipeline summary

Overview

The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions. Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk. The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file. All files are compressed with bgzip, and indexed with samtools faidx or tabix.

Steps involved:

• Download from Ensembl the GFF3 file, and the sequences of the genes in Fasta format.
• Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict.
• Compress and index the GFF3 file with bgzip and tabix.

Quick Start

1. Install Nextflow (>=22.04.0)

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).

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

   nextflow run sanger-tol/ensemblgenedownload -profile test,YOURPROFILE --outdir 
   

   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

   • The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
   • 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 in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
   • If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
   • If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

4. Start running your own analysis!

   nextflow run sanger-tol/ensemblgenedownload --input $PWD/assets/samplesheet.csv --outdir  -profile 
   

Documentation

The sanger-tol/ensemblgenedownload pipeline comes with documentation about the pipeline usage and output.

Credits

sanger-tol/ensemblgenedownload was originally written by @muffato.

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 #pipelines channel. Please create an issue on GitHub if you are not on the Sanger slack channel.

Citations

If you use sanger-tol/ensemblgenedownload for your analysis, please cite it using the following doi: 10.5281/zenodo.7183206

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.