Git Product home page Git Product logo

nexflow_pipelines's Introduction

nexflow_pipelines

Requirements:

  • nextflow (19.04)
  • JAVA >= 1.8 (Add this to your .bashrc: export NXF_JAVA_HOME=/etc/alternatives/java_sdk_1.8.0/)
  • For demultiplexing from S3: setup S3 credentials (the configuration for gis-nanopore-archive has to be your default profile, see here

To run the qcat pipeline:

nextflow qcat.nf --path s3://gis-nanopore-archive/GRIDION/N253_FLO-MIN106_SQK-LSK109/20190709_0628_GA30000_FAK66486_eb66a08d/fastq_pass/

porechop is officially retired

To run the pipeline:

nextflow  porechop.nf --path /mnt/seq/gridion/N101_FLO-MIN106_SQK-LSK108/ -resume

nexflow_pipelines's People

Contributors

lch14forever avatar

Watchers

James Cloos avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.