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