annotation-cache/downloadsnpeffcache

README

Introduction

annotation-cache/downloadsnpeffcache is a bioinformatics pipeline to download SnpEff cache.

Usage

:::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. :::

First, choose the genome you want to download the SnpEff cache for. You can find the list of the current available genomes in the shared genomes.config file.

Alternatively, you can use the following params to specify the genome and build version:

snpeff_db: "105"
snpeff_genome: "GRCh38"

Now, you can run the pipeline using:

nextflow run annotation-cache/downloadsnpeffcache \
   -profile <docker/singularity/.../institute> \
   --genome GRCh38 \
   --outdir <OUTDIR>

:::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

annotation-cache/downloadsnpeffcache was originally written by Maxime U Garcia.

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

• @adamrtalbot
• @FriederikeHanssen

Contributions and Support

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

Citations

If you use annotation-cache/downloadsnpeffcache for your analysis, please cite it using the following doi: 10.5281/zenodo.8392944

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.