{"id":32589337,"url":"https://github.com/telatin/nextflow-example","last_synced_at":"2026-02-22T21:42:46.499Z","repository":{"id":43257267,"uuid":"446375166","full_name":"telatin/nextflow-example","owner":"telatin","description":"A simple DSL2 workflow: tutorial","archived":false,"fork":false,"pushed_at":"2025-03-11T15:46:18.000Z","size":43112,"stargazers_count":26,"open_issues_count":0,"forks_count":8,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-30T00:55:18.693Z","etag":null,"topics":["denovo-assembly","nextflow","nextflow-dsl2","tutorial","tutorial-code","workflow"],"latest_commit_sha":null,"homepage":"https://telatin.github.io/microbiome-bioinformatics/Nextflow-start/","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/telatin.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2022-01-10T10:23:20.000Z","updated_at":"2025-07-07T22:06:02.000Z","dependencies_parsed_at":"2024-02-16T11:44:43.993Z","dependency_job_id":"2e9cfe89-7037-4d1c-b481-e10a0de9c485","html_url":"https://github.com/telatin/nextflow-example","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/telatin/nextflow-example","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fnextflow-example","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fnextflow-example/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fnextflow-example/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fnextflow-example/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/telatin","download_url":"https://codeload.github.com/telatin/nextflow-example/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/telatin%2Fnextflow-example/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29728500,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-22T20:09:16.275Z","status":"ssl_error","status_checked_at":"2026-02-22T20:09:13.750Z","response_time":110,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["denovo-assembly","nextflow","nextflow-dsl2","tutorial","tutorial-code","workflow"],"created_at":"2025-10-30T00:54:44.104Z","updated_at":"2026-02-22T21:42:46.492Z","avatar_url":"https://github.com/telatin.png","language":"Nextflow","readme":"[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/thanhleviet/nextflow-example/tree/2023)\n# A simple DSL2 pipeline\n\n[Nextflow](https://www.nextflow.io/) is a workflow manager that allows the creation\nof portable, scalable, reproducible pipelines.\n\nNextflow gives the possibility to separate the configuration and the logic of the\npipeline in different files.\n\nNextflow has a very strong support for different execution systems, so that you can\ntest your pipeline locally, but then deploy it in your cluster (using the installed\nscheduler, such as Slurm or PBS), or to the cloud!\n\n### :arrow_right: [**Written tutorial**](https://telatin.github.io/microbiome-bioinformatics/Nextflow-start/)\n\n## What are we doing\n\nA simple workflow to assemble prokaryotic genomes, annotate them with Prokka, and\ngathering statistics to prepare a MultiQC report.\n\nThis typical workflow processes a set of multiple samples (filtering, assemblying,\nannotating), while for other steps will collect multiple outputs to produce\na summary (QUAST for assemblys statistics, MultiQC report).\n\nBlue blocks are executed once per sample, while gray dataset are collector, and are executed\nonce per project.\n\n```mermaid\ngraph TD;\n style input fill:#ff9,stroke:#333,stroke-width:2px\n classDef collapse fill:#EEE,stroke:#333,stroke-width:2px\n classDef multi fill:#9FF,stroke:#333,troke-width:2px\n input(FASTQ INPUT) --\u003e SUBSAMPLE:::multi;\n SUBSAMPLE --\u003e FASTP:::multi;\n FASTP --\u003e ASSEMBLY:::multi;\n ASSEMBLY --\u003e QUAST:::collapse;\n ASSEMBLY --\u003e PROKKA:::multi;\n ASSEMBLY --\u003e ABRICATE:::multi;\n ASSEMBLY --\u003e MLST:::multi;\n ABRICATE --\u003e SUMMARY:::collapse;\n SUMMARY --\u003e MULTIQC:::collapse;\n MLST --\u003e MULTIQC:::collapse;\n QUAST --\u003e MULTIQC;\n PROKKA --\u003e MULTIQC;\n```\n## Resources\n\n* [Learning Nextflow in 2022](https://www.nextflow.io/blog/2022/learn-nextflow-in-2022.html), blog post by Evan Floden \u0026 Alain Coletta\n* [Nextflow tutorial (Carpentries)](https://carpentries-incubator.github.io/workflows-nextflow/index.html)\n* [nf-core community](https://nf-co.re/), a set of high quality bioinformatics pipeline backed by a fantastic community: the pipelines, their YouTube channel and their Slack channels are all worth checking \n* [Video: introduction to MultiQC](https://www.youtube.com/watch?v=BbScv9TcaMg\u0026ab_channel=PhilEwels), MultiQC is a great tool that makes any pipeline better, and Nextflow can make great use of it\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftelatin%2Fnextflow-example","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftelatin%2Fnextflow-example","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftelatin%2Fnextflow-example/lists"}