{"id":25977666,"url":"https://github.com/juke34/biten","last_synced_at":"2026-02-16T10:35:47.965Z","repository":{"id":227840687,"uuid":"772490469","full_name":"Juke34/BiTeN","owner":"Juke34","description":"A Bioinformatics Nextflow Pipeline Template","archived":false,"fork":false,"pushed_at":"2025-03-14T13:00:32.000Z","size":2622,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-09T04:11:27.421Z","etag":null,"topics":["bioinformatics","nextflow","pipelines","template","training"],"latest_commit_sha":null,"homepage":"","language":"Nextflow","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/Juke34.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","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,"publiccode":null,"codemeta":null}},"created_at":"2024-03-15T09:46:10.000Z","updated_at":"2025-08-28T10:16:27.000Z","dependencies_parsed_at":null,"dependency_job_id":"ccf97b6f-8d1a-4557-bf9a-e3489480f14b","html_url":"https://github.com/Juke34/BiTeN","commit_stats":null,"previous_names":["juke34/biten"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Juke34/BiTeN","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2FBiTeN","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2FBiTeN/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2FBiTeN/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2FBiTeN/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Juke34","download_url":"https://codeload.github.com/Juke34/BiTeN/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2FBiTeN/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29506156,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-16T09:05:14.864Z","status":"ssl_error","status_checked_at":"2026-02-16T08:55:59.364Z","response_time":115,"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":["bioinformatics","nextflow","pipelines","template","training"],"created_at":"2025-03-05T04:38:50.246Z","updated_at":"2026-02-16T10:35:47.937Z","avatar_url":"https://github.com/Juke34.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"img/biten.png\" width=\"200\" height=\"124\" /\u003e\n\n\u003ch2\u003e\u003cem\u003eBi\u003c/em\u003eoinformatics \u003cem\u003eTe\u003c/em\u003emplate in \u003cem\u003eNe\u003c/em\u003extflow\u003c/h2\u003e  \n\n\u003cimg align=\"right\" src=\"img/IRD.png\" width=\"200\" height=\"66\" /\u003e \u003cimg align=\"right\" src=\"img/MIVEGEC.png\" width=\"100\" height=\"66\" /\u003e  \n\nBiTeN is a short pipeline written in nextflow that aims to be used as a template for nextflow pipeline development.  \n\nNextflow is a free, open source software project that facilitates the execution of a computational workflow consisting of a series of interconnected steps/tasks. Utilizing Nextflow can take various forms. This repository offers a specific example illustrating how a bioinformatician can organize their code to be executed using Nextflow.\n\n## Table of Contents\n\n   * [Foreword](#foreword)\n     * [Project layout](#project-layout)\n     * [Helping to develop](#helping-to-develop)\n   * [Installation](#installation)\n      * [BiTeN](#biten)\n      * [Nextflow](#nextflow)\n      * [Container platform](#container-platform)\n        * [Docker](#docker)\n        * [Singularity](#singularity)  \n   * [Usage and test](#usage)\n   * [Parameters](#parameters)\n   * [Uninstall](#uninstall)\n   * [Contributing](#contributing)\n   * [Report bugs and issues](#report-bugs-and-issues)\n   * [How to cite?](#how-to-cite)\n   * [Acknowledgement](#acknowledgement)\n\n## Foreword\n\nThe pipeline and the whole repository (readme/Contributing/etc) can be use as template for nextflow pipeline projects.\nComment in pipeline's code help the user to better understand the different usages. \n\nThis pipeline template follow the following steps:\n\n- handling parameters, file input and help (Deal with gz and not gz file, deal with paired and unpaired input reads, etc.)\n- QC\n- Alignment\n- file conversion (sam2bam)\n- file sorting (samtools_sort)\n\n### Project layout\n    \n    BiTeN/\n    ├── README.md               # Documentation that gives users a detailed description of a project and with guidelines on how to use it.\n    ├── LICENSE                 # Lience of your projet. Licenses are important for open-source projects because they set the legal terms and conditions for using, distributing, and modifying the software\n    ├── CONTRIBUTING.md         # Provides potential project contributors with a short guide to how they can help with your project \n    ├──  img                    # Folder containing images used by the README\n    |\n    |         // FROM HERE IT IS RELATED TO THE NEXTFLOW PIPELINE\n    |\n    ├── main.nf                # The nextflow main executable file use to run your pipeline. It contains the logic of your pipeline\n    ├── modules/               # Modules folder contains components that can be included in workflows. Think as functions in programming languages. Module were introduced in DSL2. See https://www.nextflow.io/docs/latest/module.html It is encouraged to have a module file by tool.\n    │   ├── bowtie2.nf         # A module file containings processes (the basic processing primitive to execute a user script see https://www.nextflow.io/docs/latest/process.html#processes) related to the bowtie2 tool.\n    │   ├── fastqc.nf          # A module file containings processes related to the fastqc tool.\n    │   ├── samtools.nf        # A module file containings processes related to the samtools tool.\n    │   └── template.nf        # A template module file.\n    ├── subworkflows/          # Subworkflows folder contains workflow components that can be included in other workflows, typically used by the main workflow in the main.nf \n    ├── nextflow.config        # Configuration file. Nextflow has multiple way to handle config ((see here)[https://www.nextflow.io/docs/latest/config.html#configuration-file]). We can define it this file, parameters, profiles, etc.\n    ├── ressources/            # Contains configuration files that define the differents ressources i.e. computing and tools\n    │   ├── computing/         # Contains configuration files that define the computing ressources that will be loaded via profiles\n    │   │   ├── hpc.config     # A hpc configuration that define computing ressource on HPC (CPU, TimeOut, RAM per process/label and other information like parallelisation and scheduler)\n    │   │   └── local.config   # A local configuration that define computing ressource on local machine (CPU, TimeOut, RAM per process/label).\n    │   └── softwares.config   # A software configuration that define where Nextflow have to fetch the container of each tool.\n    └── test                   # Folder containing a test data set \n        ├── reads.fastq.gz\n        └── genome.fa\n\n\n### Helping to develop\n\n**Documentation**\n\n * [Nextflow Documentation](https://www.nextflow.io/docs/latest/index.html) The official nextflow documentation very well written. Do not hesitate to extensively use the search bar!\n * [Nextflow Cheat Sheet](https://github.com/danrlu/nextflow_cheatsheet/blob/main/nextflow_cheatsheet.pdf) A nice nextflow cheat sheet made by @dabrlu .\n * [Basic pipeline example from nextflow.io](https://www.nextflow.io/example1.html) Do not hesitate to look at other examples\n\n**Training**\n * [Nextflow Training from Fundamentals to Advanced](https://training.nextflow.io/latest/) The offical trainings from nextflow.io.\n * [Nextflow workshop for beginners - by vagkaratzas](https://github.com/vagkaratzas/nextflow-beginners-workshop)\n * [nf-core Training - by Zemzemfiras1](https://github.com/Zemzemfiras1/nf-core-pre-hackathon_training2025)\n * [Software Carpentry Nextflow training](https://carpentries-incubator.github.io/workflows-nextflow/index.html). High quality course made by the [Software Carpentry](https://software-carpentry.org).\n * [Bioinformatics Workshop on Tools for Reproducible Research - Nextflow](https://southgreenplatform.github.io/training_reproducible_research/pages/nextflow/nextflow-1-introduction/) A course based on [NBIS material](https://github.com/NBISweden/workshop-reproducible-research) to learn Nextflow basics.\n\n**Community**\n\n * [Nextflow Slack](https://www.nextflow.io/slack-invite.html)\n * [Nf-core](https://nf-co.re/) A community effort to collect a curated set of analysis pipelines built using Nextflow.\n * [Seqera Community](https://community.seqera.io/)\n\n**Monitoring Nextflow Pipeline**\n\n * [nf-tower](https://github.com/seqeralabs/nf-tower)\n * [nf-shard](https://github.com/gluonfield/nf-shard)\n\n## Installation\n\nThe prerequisites to run the pipeline are:  \n\n  * The BiTeN repository\n  * [Nextflow](https://www.nextflow.io/)  \u003e= 22.04.0\n  * [Docker](https://www.docker.com) or [Singularity](https://sylabs.io/singularity/) \n\n### BiTeN \n\n```bash\n# clone the workflow repository\ngit clone https://github.com/Juke34/BiTeN.git\n\n# Move in it\ncd BiTeN\n```\n\n### Nextflow \n\n  * Via conda \n\n    \u003cdetails\u003e\n      \u003csummary\u003eSee here\u003c/summary\u003e\n      \n      ```\n      conda create -n nextflow\n      conda activate nextflow\n      conda install nextflow\n      ```  \n    \u003c/details\u003e\n\n  * Manually\n    \u003cdetails\u003e\n      \u003csummary\u003eSee here\u003c/summary\u003e\n       Nextflow runs on most POSIX systems (Linux, macOS, etc) and can typically be installed by running these commands:\n\n      ```\n      # Make sure 11 or later is installed on your computer by using the command:\n      java -version\n\n      # Install Nextflow by entering this command in your terminal(it creates a file nextflow in the current dir):\n      curl -s https://get.nextflow.io | bash \n\n      # Add Nextflow binary to your user's PATH:\n      mv nextflow ~/bin/\n      # OR system-wide installation:\n      # sudo mv nextflow /usr/local/bin\n      ```\n    \u003c/details\u003e\n\n### Container platform\n\nTo run the workflow you will need a container platform: docker or singularity.\n\n### Docker\n\nPlease follow the instructions at the [Docker website](https://docs.docker.com/desktop/)\n\n### Singularity\n\nPlease follow the instructions at the [Singularity website](https://docs.sylabs.io/guides/latest/admin-guide/installation.html)\n\n## Usage\n\nYou can first check the available options and parameters by running:\n`nextflow run BiTeN.nf --help`\n\nTo run the workflow you must select a profile according to the container platform you want to use:   \n- `singularity`, a profile using Singularity to run the containers\n- `docker`, a profile using Docker to run the containers\n\nThe command will look like that: \n```\nnextflow run main.nf -profile docker \u003crest of paramaters\u003e\n```\nAnother profile is available (/!\\\\Work in progress):\n\n- `slurm`, to add if your system has a slurm executor (local by default) \n\nThe use of the `slurm` profile  will give a command like this one: \n```\nnextflow run main.nf -profile docker,slurm \u003crest of paramaters\u003e\n```\n\n## Test the workflow\n\nTest data are included in the BiTeN repository in the `test` folder.\n\nA typical command to run a test on single end data will look like that:\n\n```\nnextflow run -profile local,docker main.nf --genome test/genome.fa --reads test --single_end true\n```\n\nOn success you should get a message looking like this:\n```\n  BiTeN Pipeline execution summary\n    --------------------------------------\n    Completed at : 2024-03-07T21:40:23.180547+01:00\n    UUID         : e2a131e3-3652-4c90-b3ad-78f758c06070\n    Duration     : 8.4s\n    Success      : true\n    Exit Status  : 0\n    Error report : -\n```\n\n## Parameters\n\n| Parameter | Comment |\n| --- | --- |\n| --help           | prints the help section |\n| --reads          | path to the directory containing the reads |\n| --pattern_reads  | pattern to match the read files. In the case of single end data it would looks like: \"*.fastq.gz\". In the case of paired end data it would looks like: \"*_{R1,R2}_001.fastq.gz\" or \"*_{1,2}.fastq.gz\" |\n| --single_end     | Boolean to inform if we have a single end or paired end data. |\n| --stranded       | Boolean to inform if we have a single or stranded data. |\n|  --genome        | path to the genome file in fasta format. |\n| --bowtie2_options | Parameter to tune the bowtie2 aligner behaviour. |\n\n## Contributing\n\nWe welcome contributions from the community! See our [Contributing guidelines](https://github.com/Juke34/BiTeN/blob/main/CONTRIBUTING.md)\n\n## Report bugs and issues\n\nFound a bug or have a question? Please open an [issue](https://github.com/Juke34/BiTeN/issues).\n\n## How to cite?\n\nIf you use this template for your developement please cite or acknowledge e.g.\n\nDevelopment based on the BiTeN template (https://github.com/Juke34/BiTeN), Dainat J. \u003chere put commit version\u003e \n\n# Acknowledgement\n\nJacques Dainat (@Juke34)\nJuliette Hayer (@jhayer)\nMahesh Binzer-Panchal (@mahesh-panchal)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fbiten","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjuke34%2Fbiten","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fbiten/lists"}