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Cloudgene 3

Turn Your Nextflow Pipeline into a Powerful Web Service

Getting Started Installation Source

Documentation of Cloudgene 2

  • Build your analysis pipeline in Nextflow
  • Integrate your analysis pipeline into Cloudgene by writing a simple configuration file
  • Get a powerful web application with user management, data transfer, error handling and more
  • Deploy your application with one click to in-house clusters or public Clouds like Amazon AWS
  • Offer your application as SaaS to other scientists, managing thousands of jobs
  • Share your application, enabling others to clone your service to their own hardware or private cloud instance

Integrate Your Nextflow pipelines

id: fetch-ngs
name: FetchNGS
description: Pipeline to fetch metadata and raw FastQ files from public databases
version: 1.12.0
website: https://github.com/nf-core/fetchngs
workflow:
  steps:
    - name: Fetch NGS
      script: nf-core/fetchngs
      revision: 1.12.0

  inputs:
    - id: input
      description: IDs
      type: textarea
      value: "SRR12696236"
      writeFile: "ids.csv"

  outputs:
    - id: outdir
      description: Output
      type: local-folder

Combine Your Nextflow pipeline with others

id: fetch-ngs
name: FetchNGS
description: Pipeline to fetch metadata and raw FastQ files from public databases
version: 1.12.0
website: https://github.com/nf-core/fetchngs
author: Harshil Patel, Moritz E. Beber and Jose Espinosa-Carrasco
logo: https://raw.githubusercontent.com/nf-core/fetchngs/master/docs/images/nf-core-fetchngs_logo_light.png

workflow:
steps:
  - name: Fetch Data
    type: nextflow #set default?
    script: nf-core/fetchngs
    revision: 1.12.0
    stdout: true # set deafault?
    params:
      input: "${input_ids}"

  - name: Run Kraken2 using taxprofiler
    type: nextflow #set default?
    script: nf-core/taxprofiler
    revision: 1.1.8
    stdout: true # set deafault?
    params:
      input: "${outdir}/samplesheet/samplesheet.csv"
      run_kraken2: true
      databases: "https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_full_v1.2.csv"

inputs:
  - id: input_ids
    description: IDs
    type: textarea
    writeFile: "ids.csv"
    serialize: false

outputs:
  - id: outdir
    description: Output
    type: local-folder

Who uses Cloudgene?

Michigan Imputation Server

mtDNA-Server

Citation

Schönherr S, Forer L, Weißensteiner H, Kronenberg F, Specht G, Kloss-Brandstätter A. Cloudgene: a graphical execution platform for MapReduce programs on private and public clouds. BMC Bioinformatics. 2012 Aug 13;13:200. doi: 10.1186/1471-2105-13-200. PMID: 22888776; PMCID: PMC3532373.

About

Cloudgene has been created by Lukas Forer and Sebastian Schönherr and is MIT Licensed.

@lukfor @seppinho

Thanks to all the contributors to help us maintaining and improving Cloudgene!