nf-core/references

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Introduction

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

For most common organisms references will be stored them in the cloud, similar to AWS iGenomes, to allow for fast and simple access and better reproducibility. References can also be built locally for any organisms.

DNASEQ

For DNASEQ pipelines (ie nf-core/sarek), needing only a fasta file, it will be able to build the following references:

• BWA-MEM index
• BWA-MEM2 index
• DragMap hashtable
• Fasta dictionary (with GATK4)
• Fasta fai (with SAMtools)
• Fasta intervals bed (with GATK4)
• MSISensorPro list
• SNAP index

It will compress VCF files, if it was not already compressed, and tabix index it.

• Tabix

And with metadata, it will be able to download annotation caches from:

• EnsemblVEP
• snpEff

RNASEQ

For RNASEQ pipelines (ie nf-core/rnaseq or nf-core/rnavar), providing additional files describing genes’ structures (either GFF3 or GTF), it will be able to build the following references:

• Bowtie1 index
• Bowtie2 index
• Fasta dictionary (with GATK4)
• Fasta sizes (with SAMtools)
• GTF (from GFF3 with GffRead)
• HISAT2 index
• Kallisto index
• RSEM index
• STAR index
• Salmon index
• Splice sites (with HISAT2)
• Transcript fasta (with RSEM)

Datasheets

Datasheets are stored in references-datasheets.

Running

asset.yml:

- genome: GRCh38_chr21
  fasta: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa"
  gtf: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf"
  source_version: "CUSTOM"
  readme: "https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md"
  source: "nf-core/references"
  source_vcf: "GATK_BUNDLE"
  species: "Homo_sapiens"
  vcf: "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"

Each line represents a source for building a reference, a reference already built, or metadata.

Now, you can run the pipeline using:

nextflow run nf-core/references \
   -profile <docker/singularity/.../institute> \
   --input datasheet.yml \
   --outdir <OUTDIR>

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/references was originally written by Maxime U Garcia | Edmund Miller | Phil Ewels.

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

• Adam Talbot
• Friederike Hanssen
• Harshil Patel
• James Fellows Yates
• Jonathan Manning
• Nicolas Vannieuwkerke

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

If you use nf-core/references for your analysis, please cite it using the following doi: 10.5281/zenodo.14576225

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.