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ro-crate-metadata.json
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"datePublished": "2025-01-08T15:06:43+00:00",
"description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-references_logo_dark.png\">\n <img alt=\"nf-core/references\" src=\"docs/images/nf-core-references_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/references/actions/workflows/ci.yml)\n[](https://github.com/nf-core/references/actions/workflows/linting.yml)\n[](https://nf-co.re/references/results)\n[](https://doi.org/10.5281/zenodo.14576225)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/references)\n\n[](https://nfcore.slack.com/channels/references)\n[](https://twitter.com/nf_core)\n[](https://mstdn.science/@nf_core)\n[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/references** is a bioinformatics pipeline that build references, for multiple use cases.\n\nIt is primarily designed to build references for common organisms and store it on [AWS iGenomes](https://github.com/ewels/AWS-iGenomes/).\n\nFrom a fasta file, it will be able to build the following references:\n\n- Bowtie1 index\n- Bowtie2 index\n- BWA-MEM index\n- BWA-MEM2 index\n- DRAGMAP hashtable\n- Fasta dictionary (with GATK4)\n- Fasta fai (with SAMtools)\n- Fasta sizes (with SAMtools)\n- Fasta intervals bed (with GATK4)\n- MSIsensor-pro list\n\nWith an additional annotation file describing the genes (either GFF3 or GTF), it will be able to build the following references:\n\n- GTF (from GFF3 with GFFREAD)\n- HISAT2 index\n- Kallisto index\n- RSEM index\n- Salmon index\n- Splice sites (with HISAT2)\n- STAR index\n- Transcript fasta (with RSEM)\n\nWith a vcf file, it will compress it, if it was not already compressed, and tabix index it.\n\n## Assets\n\nAssets are stored in [references-assets](https://github.com/nf-core/references-assets).\n\n## Running\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n`asset.yml`:\n\n```yml\n- genome: GRCh38_chr21\n fasta: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa\"\n gtf: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf\"\n source_version: \"CUSTOM\"\n readme: \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md\"\n source: \"nf-core/references\"\n source_vcf: \"GATK_BUNDLE\"\n species: \"Homo_sapiens\"\n vcf: \"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz\"\n```\n\nEach line represents a source for building a reference, a reference already built or a metadata.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/references \\\n -profile <docker/singularity/.../institute> \\\n --input asset.yml \\\n --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> 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](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/references/usage) and the [parameter documentation](https://nf-co.re/references/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/references/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/references/output).\n\n## Credits\n\nnf-core/references was originally written by [Maxime U Garcia](https://github.com/maxulysse) | [Edmund Miller](https://github.com/edmundmiller) | [Phil Ewels](https://github.com/ewels).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Adam Talbot](https://github.com/adamrtalbot)\n- [Friederike Hanssen](https://github.com/FriederikeHanssen)\n- [Harshil Patel](https://github.com/drpatelh)\n- [Jonathan Manning](https://github.com/pinin4fjords)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#references` channel](https://nfcore.slack.com/channels/references) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n### How to hack on it\n\n0. Have docker, and Nextflow installed\n1. `nextflow run main.nf`\n\n### Some thoughts on reference building\n\n- We could use the glob and if you just drop a fasta in s3 bucket it'll get picked up and new resources built\n - Could take this a step further and make it a little config file that has the fasta, gtf, genome_size etc.\n- 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.\n- How much effort is too much effort?\n - Should it be as easy as adding a file on s3?\n - 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\n - So like mulled biocontainers, just make a PR to the samplesheet and boom new reference in the s3 bucket if it's approved?\n\n### Roadmap\n\nPoC for v1.0:\n\n- Replace aws-igenomes\n - bwa, bowtie2, star, bismark need to be built\n - fasta, gtf, bed12, mito_name, macs_gsize, blacklist, copied over\n\nOther nice things to have:\n\n- Building our test-datasets\n- Down-sampling for a unified genomics test dataset creation, (Thinking about viralitegration/rnaseq/wgs) and spiking in test cases of interest (Specific variants for example)\n\n## Citations\n\nIf you use nf-core/references for your analysis, please cite it using the following doi: [10.5281/zenodo.14576225](https://doi.org/10.5281/zenodo.14576225)\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
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