{"id":41034957,"url":"https://github.com/maxibor/corephylo","last_synced_at":"2026-01-22T10:31:51.193Z","repository":{"id":89839852,"uuid":"563390415","full_name":"maxibor/corephylo","owner":"maxibor","description":"core genome phylogenies","archived":false,"fork":false,"pushed_at":"2025-01-13T09:09:09.000Z","size":5592,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-17T09:42:40.475Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Groovy","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/maxibor.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-11-08T14:12:43.000Z","updated_at":"2024-12-18T10:30:11.000Z","dependencies_parsed_at":"2024-01-12T15:41:37.330Z","dependency_job_id":"7db41696-1670-4f8a-9f5c-c710152d9220","html_url":"https://github.com/maxibor/corephylo","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/maxibor/corephylo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fcorephylo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fcorephylo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fcorephylo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fcorephylo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/maxibor","download_url":"https://codeload.github.com/maxibor/corephylo/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fcorephylo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28661874,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-22T10:31:50.652Z","updated_at":"2026-01-22T10:31:51.188Z","avatar_url":"https://github.com/maxibor.png","language":"Groovy","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7509937.svg)](https://doi.org/10.5281/zenodo.7509937)\n\n## Introduction\n\n**maxibor/corephylo** is a bioinformatics best-practice analysis pipeline for core-genome based phylogenetic analysis.\n\n```mermaid\ngraph LR;\n    A[fasta genomes] --\u003e|Bakta \u003cbr\u003e functional annotation | B[GFF3 functional annotations]\n    B --\u003e|PANAROO \u003cbr\u003e pangenome computation| C[Fasta core genomes alignment]\n    C --\u003e|ClonalFrameML + maskrc-svg.py \u003cbr\u003e mask recombinant regions| D[Non recombinant core genomes alignment]\n    D --\u003e|IQTree \u003cbr\u003e ML phylogenetic analysis| E[ML Phylogenetic tree]\n    D --\u003e|RapidNJ \u003cbr\u003e NJ phylogenetic analysis| F[NJ Phylogenetic tree]\n    D --\u003e|SNP-sites \u003cbr\u003e SNPs extraction| G[VCF]\n    D --\u003e|snp-dists \u003cbr\u003e pairwise distance computation| H[SNPs based pairwise distance matrix]\n```\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), 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](https://www.nextflow.io/docs/latest/dsl2.html) 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](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n## Quick Start\n\n1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`\u003e=21.10.3`)\n\n2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.\n\n3. Download the pipeline and test it on a minimal dataset with a single command:\n\n   ```bash\n   nextflow run maxibor/corephylo -profile test,YOURPROFILE --bakta-db  \u003cpath-to-bakta-db\u003e --outdir \u003cOUTDIR\u003e\n   ```\n\n   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.\n\n   \u003e - 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`.\n   \u003e - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile \u003cinstitute\u003e` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.\n   \u003e - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.\n   \u003e - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.\n\n4. Start running your own analysis!\n\n   \u003c!-- TODO nf-core: Update the example \"typical command\" below used to run the pipeline --\u003e\n\n   ```bash\n   nextflow run maxibor/corephylo --genome genomesheet.csv --bakta-db  \u003cpath-to-bakta-db\u003e --outdir \u003cOUTDIR\u003e -profile \u003cdocker/singularity/podman/shifter/charliecloud/conda/institute\u003e\n   ```\n\n## Documentation\n\n- [**Usage**](docs/usage.md)\n- [**Parameters**](docs/parameters.md)\n\n## Credits\n\nmaxibor/corephylo was originally written by Maxime Borry.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\u003c!-- TODO nf-core: If applicable, make list of people who have also contributed --\u003e\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\u003c!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. --\u003e\n\n\u003c!-- If you use  maxibor/corephylo for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --\u003e\n\n\u003c!-- TODO nf-core: Add bibliography of tools and data used in your pipeline --\u003e\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).\n\n\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fcorephylo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxibor%2Fcorephylo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fcorephylo/lists"}