Cloudgene 3¶

A DSL language similar to Nextflow
Describes expected behavior using 'when' and 'then' blocks
Abundance of functions for writing elegant and readable assertions
Utilizes snapshots to write tests for complex data structures
Provides commands for generating boilerplate code
Includes a test-runner that executes these scripts
Easy installation on CI systems

Integrate Your Nextflow pipelines¶

Integrate your analysis pipeline into Cloudgene by writing a simple configuration file.

cloudgene.yaml Web-Interface Results

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: folder

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Share your application via HTTP, GitHub, or S3, and enable users to install it with a simple command.

cloudgene install lukfor/cg-fetchngs

Combine Your Nextflow pipeline with others¶

Combine your Nextflow pipeline with other pipelines and create use-case specific web services.

cloudgene.yaml Web-Interface Results

id: taxprofiler
name: Taxprofiler
description: Taxonomic classification and profiling of shotgun short- and long-read metagenomic data
version: 1.1.8
website: https://github.com/nf-core/taxprofiler
author: James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, and the nf-core/taxprofiler team
logo: https://raw.githubusercontent.com/nf-core/fetchngs/master/docs/images/nf-core-fetchngs_logo_light.png

workflow:
  steps:
    - name: Fetch Data
      script: nf-core/fetchngs
      revision: 1.12.0
      stdout: true
      params:
        input: "${input_ids}"

    - name: Run taxprofiler
      script: nf-core/taxprofiler
      revision: 1.1.8
      stdout: true
      params:
        input: "${outdir}/samplesheet/samplesheet.csv"
        databases: "https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database_full_v1.2.csv"
        multiqc_title: "${CLOUDGENE_JOB_NAME}"

  inputs:
    - id: input_ids
      description: IDs
      type: textarea
      value: "SRR12696236"
      writeFile: "ids.csv"
      serialize: false

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

alt text

Who uses Cloudgene?¶

Michigan Imputation Server 2¶

Michigan Imputation Server 2 provides a free genotype imputation service (chromosomes 1-22, chromosome X and HLA region) using Minimac4. You can upload phased or unphased GWAS genotypes and receive phased and imputed genomes in return. Our server supports imputation from numerous reference panels. For all uploaded datasets a comprehensive QC is performed. The complete source code is available on GitHub.

mtDNA-Server 2¶

mtDNA-Server 2 is a Nextflow DSL2 pipeline to accurately detect heteroplasmic and homoplasmic variants in mitochondrial (mtDNA) genomes. The complete source code can be acccessed here.

Haplocheck¶

Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content.

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!