{"id":20153429,"url":"https://github.com/nextflow-io/rnaseq-nf","last_synced_at":"2025-08-09T03:13:10.166Z","repository":{"id":22760941,"uuid":"97247330","full_name":"nextflow-io/rnaseq-nf","owner":"nextflow-io","description":"A proof of concept of RNAseq pipeline","archived":false,"fork":false,"pushed_at":"2024-11-08T21:42:12.000Z","size":601,"stargazers_count":75,"open_issues_count":9,"forks_count":104,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-01-13T12:22:38.056Z","etag":null,"topics":["genomics","nextflow","rnaseq"],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nextflow-io.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":"2017-07-14T15:20:49.000Z","updated_at":"2025-01-13T02:31:56.000Z","dependencies_parsed_at":"2023-11-06T07:24:55.724Z","dependency_job_id":"70184005-7976-4f70-8217-b3bb29142ac1","html_url":"https://github.com/nextflow-io/rnaseq-nf","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Frnaseq-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Frnaseq-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Frnaseq-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextflow-io%2Frnaseq-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextflow-io","download_url":"https://codeload.github.com/nextflow-io/rnaseq-nf/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241592984,"owners_count":19987467,"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","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":["genomics","nextflow","rnaseq"],"created_at":"2024-11-13T23:19:00.673Z","updated_at":"2025-03-03T01:23:05.089Z","avatar_url":"https://github.com/nextflow-io.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# RNAseq-NF pipeline \n\nA basic pipeline for quantification of genomic features from short read data\nimplemented with Nextflow.\n\n[![nextflow](https://img.shields.io/badge/nextflow-%E2%89%A523.04.0-brightgreen.svg)](http://nextflow.io)\n\n\n## Requirements \n\n* Unix-like operating system (Linux, macOS, etc)\n* Java 11 \n\n## Quickstart \n\n1. If you don't have it already install Docker in your computer. Read more [here](https://docs.docker.com/).\n\n2. Install Nextflow (version 23.10.0 or later):\n      \n        curl -s https://get.nextflow.io | bash\n\n3. Launch the pipeline execution: \n\n        ./nextflow run nextflow-io/rnaseq-nf -with-docker\n        \n4. When the execution completes open in your browser the report generated at the following path:\n\n        results/multiqc_report.html \n\t\nYou can see an example report at the following [link](http://multiqc.info/examples/rna-seq/multiqc_report.html).\t\n\t\nNote: the very first time you execute it, it will take a few minutes to download the pipeline \nfrom this GitHub repository and the associated Docker images needed to execute the pipeline.  \n\n## Pipeline flowchart\n\nHere is a visual representation of the design of RNASeq-NF pipeline, generated using the [visualization functionality](https://www.nextflow.io/docs/latest/tracing.html#dag-visualisation) of Nextflow.\n\n```mermaid\n%%{init: { 'theme': 'forest' } }%%\nflowchart TD\n    p0((Channel.fromFilePairs))\n    p1(( ))\n    p2[RNASEQ:INDEX]\n    p3[RNASEQ:FASTQC]\n    p4[RNASEQ:QUANT]\n    p5([concat])\n    p6([collect])\n    p7(( ))\n    p8[MULTIQC]\n    p9(( ))\n    p0 --\u003e|read_pairs_ch| p3\n    p1 --\u003e|transcriptome| p2\n    p2 --\u003e p4\n    p3 --\u003e p5\n    p0 --\u003e|read_pairs_ch| p4\n    p4 --\u003e|pair_id| p5\n    p5 --\u003e p6\n    p6 --\u003e|$out0| p8\n    p7 --\u003e|config| p8\n    p8 --\u003e p9\n```\n\n## Cluster support\n\nRNASeq-NF execution relies on [Nextflow](http://www.nextflow.io) framework which provides an \nabstraction between the pipeline functional logic and the underlying processing system.\n\nThis allows the execution of the pipeline in a single computer or in a HPC cluster without modifying it.\n\nCurrently the following resource manager platforms are supported:\n\n  + Univa Grid Engine (UGE)\n  + Platform LSF\n  + SLURM\n  + PBS/Torque\n\n\nBy default the pipeline is parallelized by spawning multiple threads in the machine where the script is launched.\n\nTo submit the execution to a UGE cluster create a file named `nextflow.config` in the directory\nwhere the pipeline is going to be executed with the following content:\n\n    process {\n      executor='uge'\n      queue='\u003cqueue name\u003e'\n    }\n\nTo lean more about the avaible settings and the configuration file read the \nNextflow [documentation](http://www.nextflow.io/docs/latest/config.html).\n\n\n## Components \n\nRNASeq-NF uses the following software components and tools: \n\n* [Salmon](https://combine-lab.github.io/salmon/)\n* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n* [MultiQC](https://multiqc.info)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextflow-io%2Frnaseq-nf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextflow-io%2Frnaseq-nf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextflow-io%2Frnaseq-nf/lists"}