Introduction

nf-core/references is a bioinformatics pipeline that build references.

How to hack on it

0. Have docker, and Nextflow installed
1. nextflow run main.nf

Some thoughts on reference building:

• We could use the glob and if you just drop a fasta in s3 bucket it'll get picked up and new resources built
  • Could take this a step further and make it a little config file that has the fasta, gtf, genome_size etc.
• How do we avoid rebuilding? Ideally we should build once on a new minor release of an aligner/reference. IMO kinda low priority because the main cost is going to be egress, not compute.
• How much effort is too much effort?
  • Should it be as easy as adding a file on s3?
    • No that shouldn't be a requirement, should be able to link to a reference externally(A "source of truth" ie an FTP link), and the workflow will build the references
    • So like mulled biocontainers, just make a PR to the samplesheet and boom new reference in the s3 bucket if it's approved?

Roadmap

PoC:

• Replace aws-igenomes
  • bwa, bowtie2, star, bismark need to be built
  • fasta, gtf, bed12, mito_name, macs_gsize blacklist, copied over

Other nice things to have:

• Building our test-datasets
• Downsampling for a unified genomics test dataset creation, (Thinking about viralitegration/rnaseq/wgs) and spiking in test cases of interest(Specific variants for example)

Credits

nf-core/references was originally written by @maxulysse | @edmundmiller | @ewels.

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

• @adamrtalbot
• @drpatelh
• @FriederikeHanssen
• @pinin4fjords

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 #references channel (you can join with this invite).

Citations

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

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.