{"id":30238026,"url":"https://github.com/seqeralabs/nf-chai","last_synced_at":"2025-08-15T02:59:36.715Z","repository":{"id":263813485,"uuid":"891427427","full_name":"seqeralabs/nf-chai","owner":"seqeralabs","description":"POC Nextflow pipeline to run the Chai-1, SOTA model for biomolecular structure prediction","archived":false,"fork":false,"pushed_at":"2025-01-16T18:26:57.000Z","size":13218,"stargazers_count":11,"open_issues_count":2,"forks_count":5,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-08-10T05:59:37.205Z","etag":null,"topics":["nextflow","pipeline","protein-structure","structure-prediction"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/seqeralabs.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":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-11-20T10:11:45.000Z","updated_at":"2025-03-16T17:08:48.000Z","dependencies_parsed_at":"2024-11-20T12:55:38.595Z","dependency_job_id":null,"html_url":"https://github.com/seqeralabs/nf-chai","commit_stats":null,"previous_names":["seqeralabs/nf-chai"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/seqeralabs/nf-chai","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqeralabs%2Fnf-chai","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqeralabs%2Fnf-chai/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqeralabs%2Fnf-chai/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqeralabs%2Fnf-chai/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqeralabs","download_url":"https://codeload.github.com/seqeralabs/nf-chai/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqeralabs%2Fnf-chai/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270515668,"owners_count":24598440,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-15T02:00:12.559Z","response_time":110,"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":["nextflow","pipeline","protein-structure","structure-prediction"],"created_at":"2025-08-15T02:59:15.240Z","updated_at":"2025-08-15T02:59:36.694Z","avatar_url":"https://github.com/seqeralabs.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nf-chai\n\n[![GitHub Actions CI Status](https://github.com/seqeralabs/nf-chai/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-chai/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-chai/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-chai/actions/workflows/linting.yml)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/seqeralabs/nf-chai)\n\n## POC implementation of Chai-1 in Nextflow\n\n## Introduction\n\n**nf-chai** is a simple, proof-of-concept bioinformatics pipeline for running the [Chai-1](https://github.com/chaidiscovery/chai-lab) protein prediction algorithm on an input set of protein sequences in FASTA format. The pipeline has been written in Nextflow to generate results for downstream analysis in a reproducible, scalable and portable way.\n\n## Usage\n\n\u003e [!NOTE]\n\u003e If you are new to Nextflow, 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\nFirst, prepare a FASTA file with entities supported by Chai-1 in the format highlighted below. You can also provide a directory with multiple FASTA files by specifying the `--input` parameter with a directory path like this: `--input \"/path/to/fasta_files/*.fasta|*.fa\"`.\n\n`multiple_entities.fa`:\n\n```txt\n\u003eprotein|name=example-of-long-protein\nAGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQWMFGCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP\n\u003eprotein|name=example-of-short-protein\nAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM\n\u003eprotein|name=example-peptide\nGAAL\n\u003eligand|name=example-ligand-as-smiles\nCCCCCCCCCCCCCC(=O)O\n```\n\nRun the pipeline using CPUs with the command below:\n\n```bash\nnextflow run seqeralabs/nf-chai \\\n   --input multiple_entities.fa \\\n   --outdir \u003cOUTDIR\u003e \\\n   -profile \u003cdocker/singularity\u003e\n```\n\nRun the pipeline using GPUs with the command below:\n\n```bash\nnextflow run seqeralabs/nf-chai \\\n   --input multiple_entities.fa \\\n   --outdir \u003cOUTDIR\u003e \\\n   --use_gpus \\\n   -profile \u003cdocker/singularity\u003e\n```\n\nSet the `--weights_dir` parameter to a location with the pre-downloaded weights required by Chai-1 to avoid having to download them every time you run the pipeline.\n\nTo further improve prediction performance using pre-built multiple sequence alignments (MSA) with evolutionary information, set the `--msa_dir` parameter to a location with [`*.aligned.pqt`](https://github.com/chaidiscovery/chai-lab/tree/main/examples/msas#adding-msa-evolutionary-information) format as required by Chai-1.\n\n## Credits\n\nnf-chai was originally written by the Seqera Team.\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\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/main/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%2Fseqeralabs%2Fnf-chai","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqeralabs%2Fnf-chai","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqeralabs%2Fnf-chai/lists"}