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@Eco-Flow

Eco-Flow

README.md

What is Eco-Flow?

Eco-Flow is a UCL based research initiative to develop agri-ecology specific modern, reproducible and scalable data pipelines.

Eco-Flow wants to do more than just build pipelines, we want to cultivate a healthy community of people who share similar research within agri-ecology who can help support each other with their research and analysis.

This community is centered around the pipelines developed by the Eco-Flow team. The pipelines developed will be requested by the community.

If you would like to join the community then please email ecoflowucl [at] gmail.com.

Or start a community discussion about a potential pipeline by creating a new issue on Eco-Flow/pipeline-discussions.

Who are we?

Project lead : Chris Wyatt

Chris is a senior bioinformatician on the project, with a background in omic technologies and pipeline development.



Ecology Advisor : Seirian Sumner

Professor Seirian Sumner is a leading researcher in ecology and genomics.


Bioinformatics Advisor : Yannick Wurm

Professor Yannick Wurm is a data scientist expert on genome analysis and evolution.



Former members

Technical lead : Simon Murray

Simon is a senior bioinformatician on the project, with a background in pipeline development and containerisation. Simon moved to Genomics England (May 2024)


Where can I found out more?

All the Eco-Flow information can be found on our website: https://eco-flow.github.io.

What is special about our Pipelines?

We intend to develop novel, gold standard Nextflow pipelines for the agri-ecology field. These pipelines will fully adhere to the nf-core community guidelines, have complete unit testing with nf-test and use containerised environments published to our quay.io space: quay.io/user/ecoflowucl.

The intention if for all our pipelines to be deployable in any environment (local, on-prem HPC or cloud) utilising either Docker or Singularity for containerisation.

At Eco-Flow we want to help make deploying large-scale bioinformatics pipelines as easy for you as possible which is why everything we produce is public. This includes the configuration files for specific on-premise HPCs. If you want to see if we have already configured Nextflow for you HPC then check out Eco-Flow/configs.

Published Pipelines

  • Eco-Flow/synteny - A pipeline that compares gene synteny between chromosome level genome assemblies.

Popular repositories Loading

  1. synteny synteny Public

    A Nextflow pipeline for running synteny analysis.

    Perl 12 2

  2. Eco-Flow.github.io Eco-Flow.github.io Public

    Eco-Flow webpage

    4 2

  3. excon excon Public

    A pipeline to measure gene family expansion and contraction

    Perl 3 1

  4. training training Public

    A repository to run training courses

    Shell 3 1

  5. configs configs Public

    A repository to store config files set up for specific HPCs.

    1 1

  6. docker-build docker-build Public

    A repository containing Dockerfiles for containers used within Eco-Flow's Nextflow pipelines.

    Dockerfile 1

Repositories

Showing 10 of 13 repositories
  • genomeqc Public
    Eco-Flow/genomeqc’s past year of commit activity
    Nextflow 0 MIT 0 5 0 Updated Oct 6, 2024
  • test-datasets Public Forked from nf-core/test-datasets

    Test data to be used for automated testing with the nf-core pipelines

    Eco-Flow/test-datasets’s past year of commit activity
    0 MIT 340 0 0 Updated Oct 6, 2024
  • synteny Public

    A Nextflow pipeline for running synteny analysis.

    Eco-Flow/synteny’s past year of commit activity
    Perl 12 2 17 0 Updated Oct 3, 2024
  • excon Public

    A pipeline to measure gene family expansion and contraction

    Eco-Flow/excon’s past year of commit activity
    Perl 3 MIT 1 14 0 Updated Sep 19, 2024
  • modules Public Forked from nf-core/modules

    Repository to host tool-specific module files for the Nextflow DSL2 community!

    Eco-Flow/modules’s past year of commit activity
    Nextflow 0 MIT 695 0 0 Updated Sep 6, 2024
  • pollen-metabarcoding Public

    A pipeline developled in collaboration with Exeter University

    Eco-Flow/pollen-metabarcoding’s past year of commit activity
    Nextflow 1 0 5 0 Updated Aug 30, 2024
  • comparete Public

    A pipeline to compare TE content across genomes

    Eco-Flow/comparete’s past year of commit activity
    Perl 0 MIT 0 6 0 Updated Aug 25, 2024
  • training Public

    A repository to run training courses

    Eco-Flow/training’s past year of commit activity
    Shell 3 MIT 1 3 0 Updated Aug 20, 2024
  • docker-build Public

    A repository containing Dockerfiles for containers used within Eco-Flow's Nextflow pipelines.

    Eco-Flow/docker-build’s past year of commit activity
    Dockerfile 1 MIT 0 0 0 Updated Aug 19, 2024
  • Eco-Flow.github.io Public

    Eco-Flow webpage

    Eco-Flow/Eco-Flow.github.io’s past year of commit activity
    4 2 0 0 Updated Aug 17, 2024
View all repositories

People

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